xps import data derived from different batches
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Steve Shen ▴ 330
@steve-shen-3743
Last seen 10.3 years ago
Dear Christian, Just couldn't figure out what exactly problem is, but maybe you can point out easily. I have a set of cel files which derived from two different batches. I tried to import data with one command line, but it didn't work (the error message is below) and getTreeNames give me an error says "object 'xxx.root' not found", but root file is actually in the folder. I then import first batch cel files first and use addData command to import second batch. It turned out that the importdata command worked well as expected, but addData command generated same exact error message as first time (see below). However, this time the getTreeNames worked. The commands and errors are appended. Thanks, Steve ###import two batches > data.xps <- import.data(scheme.mogene10st, "gm_dk_phase2", filedir = datdir, celfiles= celfiles, celnames=celnames) [[alternative HTML version deleted]]
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Steve Shen ▴ 330
@steve-shen-3743
Last seen 10.3 years ago
Sorry, misclick! On Sun, Mar 7, 2010 at 9:46 PM, Steve Shen <sshen@bu.edu> wrote: > Dear Christian, > > Just couldn't figure out what exactly problem is, but maybe you can point > out easily. I have a set of cel files which derived from two different > batches. I tried to import data with one command line, but it didn't work > (the error message is below) and getTreeNames give me an error says "object > 'xxx.root' not found", but root file is actually in the folder. > > I then import first batch cel files first and use addData command to import > second batch. It turned out that the importdata command worked well as > expected, but addData command generated same exact error message as first > time (see below). However, this time the getTreeNames worked. > > The commands and errors are appended. Thanks, > > Steve > > > ###import two batches > > data.xps <- import.data(scheme.mogene10st, "gm_dk_phase2", filedir = > datdir, celfiles= celfiles, celnames=celnames) > Errors, (see below) > getTreeNames(rootFile(data.xps)) Error: object 'data.xps' not found Error in rootFile(data.xps) : error in evaluating the argument 'object' in selecting a method for function 'rootFile' ###import first batch first, then add > data.gm.dk.xps <- import.data(scheme.mogene10st, "gm_dk_phase2", filedir=datdir, celdir=celdir, celfiles=celfiles, celnames=celnames) #no errors > data.gm.dk.xps <- addData(data.gm.dk.xps, celdir=celdir, celfiles=celfiles02, celnames=celnames02) Error in .local(object, ...) : error in function ‘ImportData’ Opening file <~/XPS/scheme/Scheme_MoGene10stv1r4_na30.root> in <read> mode... Opening file <~/XPS/ROOTdata/gm_dk_phase2_cel.root> in <update> mode... Importing <~/Projects/DKotton_Gustavo/PhaseII/DK_A7_07.CEL> as <dk_a7_07.cel>... hybridization statistics: 1 cells with minimal intensity 18 1 cells with maximal intensity 11987 Importing <~/Projects/DKotton_Gustavo/PhaseII/DK_A8_08.CEL> as <dk_a8_08.cel>... hybridization statistics: 17 cells with minimal intensity 21 1 cells with maximal intensity 13337 Importing <~/DKotton_Gustavo/PhaseII/DK_B1_09.CEL> as <dk_b1_09.cel>... hybridization statistics: 2 cells with minimal intensity 19 1 cells with maximal intensity 11798 Importing <~/Projects/DKotton_Gustavo/PhaseII/DK_A4_04.CEL> as <dk_a4_04.cel>... hybridization statistics: 27 cells with minimal intensity 19 1 cells with maximal intensity 14787 Importing <~/Projects/DKotton_Gustavo/PhaseII/DK_A5_05.CEL> as <dk_a5_05.cel>... Error: Header line of file </users> is not correct. hybridization statistics: 7 cells with minimal intensity 20 1 cells with maximal intensity 15474 Importing <~/Projects/DKotton_Gustavo/PhaseII/DK_A3_03.CEL> as <dk_a3_03.cel>... hybridization statistics: 1 cells with minimal intensity 20 1 cells with maximal intensity 12507 [[alternative HTML version deleted]]
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The problem seems to related to one of the cel files, error says: Error: Header line of file <~/Projects/DKotton_Gustavo/PhaseII/DK_A1_01.CEL> is not correct. What does this mean? To me all .cel files are same. Best, Steve On Sun, Mar 7, 2010 at 9:51 PM, Steve Shen <sshen@bu.edu> wrote: > Sorry, misclick! > > On Sun, Mar 7, 2010 at 9:46 PM, Steve Shen <sshen@bu.edu> wrote: > >> Dear Christian, >> >> Just couldn't figure out what exactly problem is, but maybe you can point >> out easily. I have a set of cel files which derived from two different >> batches. I tried to import data with one command line, but it didn't work >> (the error message is below) and getTreeNames give me an error says "object >> 'xxx.root' not found", but root file is actually in the folder. >> >> I then import first batch cel files first and use addData command to >> import second batch. It turned out that the importdata command worked well >> as expected, but addData command generated same exact error message as first >> time (see below). However, this time the getTreeNames worked. >> >> The commands and errors are appended. Thanks, >> >> Steve >> >> > >> ###import two batches > > > >> > data.xps <- import.data(scheme.mogene10st, "gm_dk_phase2", filedir = >> datdir, celfiles= celfiles, celnames=celnames) >> > Errors, (see below) > > getTreeNames(rootFile(data.xps)) > Error: object 'data.xps' not found > Error in rootFile(data.xps) : > error in evaluating the argument 'object' in selecting a method for > function 'rootFile' > > ###import first batch first, then add > > data.gm.dk.xps <- import.data(scheme.mogene10st, "gm_dk_phase2", > filedir=datdir, celdir=celdir, celfiles=celfiles, celnames=celnames) > #no errors > > data.gm.dk.xps <- addData(data.gm.dk.xps, celdir=celdir, > celfiles=celfiles02, celnames=celnames02) > Error in .local(object, ...) : error in function ‘ImportData’ > Opening file <~/XPS/scheme/Scheme_MoGene10stv1r4_na30.root> in <read> > mode... > Opening file <~/XPS/ROOTdata/gm_dk_phase2_cel.root> in <update> mode... > Importing <~/Projects/DKotton_Gustavo/PhaseII/DK_A7_07.CEL> as > <dk_a7_07.cel>... > hybridization statistics: > 1 cells with minimal intensity 18 > 1 cells with maximal intensity 11987 > Importing <~/Projects/DKotton_Gustavo/PhaseII/DK_A8_08.CEL> as > <dk_a8_08.cel>... > hybridization statistics: > 17 cells with minimal intensity 21 > 1 cells with maximal intensity 13337 > Importing <~/DKotton_Gustavo/PhaseII/DK_B1_09.CEL> as <dk_b1_09.cel>... > hybridization statistics: > 2 cells with minimal intensity 19 > 1 cells with maximal intensity 11798 > Importing <~/Projects/DKotton_Gustavo/PhaseII/DK_A4_04.CEL> as > <dk_a4_04.cel>... > hybridization statistics: > 27 cells with minimal intensity 19 > 1 cells with maximal intensity 14787 > Importing <~/Projects/DKotton_Gustavo/PhaseII/DK_A5_05.CEL> as > <dk_a5_05.cel>... > Error: Header line of file > </users> is > not correct. > hybridization statistics: > 7 cells with minimal intensity 20 > 1 cells with maximal intensity 15474 > Importing <~/Projects/DKotton_Gustavo/PhaseII/DK_A3_03.CEL> as > <dk_a3_03.cel>... > hybridization statistics: > 1 cells with minimal intensity 20 > 1 cells with maximal intensity 12507 > > [[alternative HTML version deleted]]
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The problem is indeed this CEL file. It went well if I remove this .CEL file from import list. The question is what's wrong with this file. It can be read as normal one from affy tools (e.g. expression console). If someone interested in this problem, I can attached both good and bad cel files. Thanks, Steve On Sun, Mar 7, 2010 at 10:00 PM, Steve Shen <sshen@bu.edu> wrote: > The problem seems to related to one of the cel files, error says: > > Error: Header line of file > <~/Projects/DKotton_Gustavo/PhaseII/DK_A1_01.CEL> is not correct. What does > this mean? To me all .cel files are same. > > Best, > Steve > > > > On Sun, Mar 7, 2010 at 9:51 PM, Steve Shen <sshen@bu.edu> wrote: > >> Sorry, misclick! >> >> On Sun, Mar 7, 2010 at 9:46 PM, Steve Shen <sshen@bu.edu> wrote: >> >>> Dear Christian, >>> >>> Just couldn't figure out what exactly problem is, but maybe you can point >>> out easily. I have a set of cel files which derived from two different >>> batches. I tried to import data with one command line, but it didn't work >>> (the error message is below) and getTreeNames give me an error says "object >>> 'xxx.root' not found", but root file is actually in the folder. >>> >>> I then import first batch cel files first and use addData command to >>> import second batch. It turned out that the importdata command worked well >>> as expected, but addData command generated same exact error message as first >>> time (see below). However, this time the getTreeNames worked. >>> >>> The commands and errors are appended. Thanks, >>> >>> Steve >>> >>> >> >>> ###import two batches >> >> >> >>> > data.xps <- import.data(scheme.mogene10st, "gm_dk_phase2", filedir = >>> datdir, celfiles= celfiles, celnames=celnames) >>> >> Errors, (see below) >> > getTreeNames(rootFile(data.xps)) >> Error: object 'data.xps' not found >> Error in rootFile(data.xps) : >> error in evaluating the argument 'object' in selecting a method for >> function 'rootFile' >> >> ###import first batch first, then add >> > data.gm.dk.xps <- import.data(scheme.mogene10st, "gm_dk_phase2", >> filedir=datdir, celdir=celdir, celfiles=celfiles, celnames=celnames) >> #no errors >> > data.gm.dk.xps <- addData(data.gm.dk.xps, celdir=celdir, >> celfiles=celfiles02, celnames=celnames02) >> Error in .local(object, ...) : error in function ‘ImportData’ >> Opening file <~/XPS/scheme/Scheme_MoGene10stv1r4_na30.root> in <read> >> mode... >> Opening file <~/XPS/ROOTdata/gm_dk_phase2_cel.root> in <update> mode... >> Importing <~/Projects/DKotton_Gustavo/PhaseII/DK_A7_07.CEL> as >> <dk_a7_07.cel>... >> hybridization statistics: >> 1 cells with minimal intensity 18 >> 1 cells with maximal intensity 11987 >> Importing <~/Projects/DKotton_Gustavo/PhaseII/DK_A8_08.CEL> as >> <dk_a8_08.cel>... >> hybridization statistics: >> 17 cells with minimal intensity 21 >> 1 cells with maximal intensity 13337 >> Importing <~/DKotton_Gustavo/PhaseII/DK_B1_09.CEL> as <dk_b1_09.cel>... >> hybridization statistics: >> 2 cells with minimal intensity 19 >> 1 cells with maximal intensity 11798 >> Importing <~/Projects/DKotton_Gustavo/PhaseII/DK_A4_04.CEL> as >> <dk_a4_04.cel>... >> hybridization statistics: >> 27 cells with minimal intensity 19 >> 1 cells with maximal intensity 14787 >> Importing <~/Projects/DKotton_Gustavo/PhaseII/DK_A5_05.CEL> as >> <dk_a5_05.cel>... >> Error: Header line of file >> </users> is >> not correct. >> hybridization statistics: >> 7 cells with minimal intensity 20 >> 1 cells with maximal intensity 15474 >> Importing <~/Projects/DKotton_Gustavo/PhaseII/DK_A3_03.CEL> as >> <dk_a3_03.cel>... >> hybridization statistics: >> 1 cells with minimal intensity 20 >> 1 cells with maximal intensity 12507 >> >> > [[alternative HTML version deleted]]
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Dear Steve, As you have mentioned in your last mail, you got a corrupt CEL-file which has a size of more than 10-times the usual size. This could be a missing EOF. However, the error message you get should only appear for Version=3 CEL-files, i.e. text files, which could explain the large size. Could it be that someone has converted this CEL-file from binary to text format? Could you please run the following commands: $ head -n17 DK_A1_01.CEL $ head -n17 DK_A3_03.CEL and send me the output. Best regards Christian Steve Shen wrote: > The problem is indeed this CEL file. It went well if I remove this > .CEL file from import list. The question is what's wrong with this > file. It can be read as normal one from affy tools (e.g. expression > console). If someone interested in this problem, I can attached both > good and bad cel files. > > Thanks, > Steve > > On Sun, Mar 7, 2010 at 10:00 PM, Steve Shen <sshen at="" bu.edu=""> <mailto:sshen at="" bu.edu="">> wrote: > > The problem seems to related to one of the cel files, error says: > > Error: Header line of file > <~/Projects/DKotton_Gustavo/PhaseII/DK_A1_01.CEL> is not correct. > What does this mean? To me all .cel files are same. > > Best, > Steve > > > > On Sun, Mar 7, 2010 at 9:51 PM, Steve Shen <sshen at="" bu.edu=""> <mailto:sshen at="" bu.edu="">> wrote: > > Sorry, misclick! > > On Sun, Mar 7, 2010 at 9:46 PM, Steve Shen <sshen at="" bu.edu=""> <mailto:sshen at="" bu.edu="">> wrote: > > Dear Christian, > > Just couldn't figure out what exactly problem is, but > maybe you can point out easily. I have a set of cel files > which derived from two different batches. I tried to > import data with one command line, but it didn't work (the > error message is below) and getTreeNames give me an error > says "object 'xxx.root' not found", but root file is > actually in the folder. > > I then import first batch cel files first and use addData > command to import second batch. It turned out that the > importdata command worked well as expected, but addData > command generated same exact error message as first time > (see below). However, this time the getTreeNames worked. > > The commands and errors are appended. Thanks, > > Steve > > > > ###import two batches > > > > > data.xps <- import.data(scheme.mogene10st, > "gm_dk_phase2", filedir = datdir, celfiles= celfiles, > celnames=celnames) > > Errors, (see below) > > getTreeNames(rootFile(data.xps)) > Error: object 'data.xps' not found > Error in rootFile(data.xps) : > error in evaluating the argument 'object' in selecting a > method for function 'rootFile' > > ###import first batch first, then add > > data.gm.dk.xps <- import.data(scheme.mogene10st, > "gm_dk_phase2", filedir=datdir, celdir=celdir, > celfiles=celfiles, celnames=celnames) > #no errors > > data.gm.dk.xps <- addData(data.gm.dk.xps, celdir=celdir, > celfiles=celfiles02, celnames=celnames02) > Error in .local(object, ...) : error in function ?ImportData? > Opening file <~/XPS/scheme/Scheme_MoGene10stv1r4_na30.root> in > <read> mode... > Opening file <~/XPS/ROOTdata/gm_dk_phase2_cel.root> in > <update> mode... > Importing <~/Projects/DKotton_Gustavo/PhaseII/DK_A7_07.CEL> as > <dk_a7_07.cel>... > hybridization statistics: > 1 cells with minimal intensity 18 > 1 cells with maximal intensity 11987 > Importing <~/Projects/DKotton_Gustavo/PhaseII/DK_A8_08.CEL> as > <dk_a8_08.cel>... > hybridization statistics: > 17 cells with minimal intensity 21 > 1 cells with maximal intensity 13337 > Importing <~/DKotton_Gustavo/PhaseII/DK_B1_09.CEL> as > <dk_b1_09.cel>... > hybridization statistics: > 2 cells with minimal intensity 19 > 1 cells with maximal intensity 11798 > Importing <~/Projects/DKotton_Gustavo/PhaseII/DK_A4_04.CEL> as > <dk_a4_04.cel>... > hybridization statistics: > 27 cells with minimal intensity 19 > 1 cells with maximal intensity 14787 > Importing <~/Projects/DKotton_Gustavo/PhaseII/DK_A5_05.CEL> as > <dk_a5_05.cel>... > Error: Header line of file > </users> > is not correct. > hybridization statistics: > 7 cells with minimal intensity 20 > 1 cells with maximal intensity 15474 > Importing <~/Projects/DKotton_Gustavo/PhaseII/DK_A3_03.CEL> as > <dk_a3_03.cel>... > hybridization statistics: > 1 cells with minimal intensity 20 > 1 cells with maximal intensity 12507 > > >
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Hi Christian, It's possible. I looked the time stamp for the files that bad one has different time stamp too. Here is what I got after command issued. Best, Steve ew-host:PhaseII ssshen$ head -n17 DK_A1_01.CEL ?0?K???UU?>??3??b???dd?D?**Ֆ?7QQ݊ ??hXd7?¢?"""?M??LoDƘ97##3?9f??s3?!DZ???cL95N}??Ύ?'?+O???w ??Z? >??"~o?K?? ??P ;.|??'??? ?zj???v?b??:ʎ??~Ҟ???S???ÿ???7?k?S?^Ozgx???鋸????????? ?ǀ????.??Be??~o??w;l???)???????=6Ǔ???>?n?k6?Y????1w?U??y?????݄??v?? gp?I?z???}\?|????????]? ??'??!3???1?/?N??=kG???$?Y?ͱ7N????{??e??d~B?????wo ;.?jy\܋???/??Z?7,????xc????ޟ??s???ݟdٻ???????>?g???4?=????~??|zEM?? g?O?'%-?~=?Ȃא*??6>?q>y??t* ?h?멏Z?????>??V??>??ƽc?'????q???????Os݌???#k????x??|??????ِA?񪃉Q??z_~?G???kN?l?X ?0p???????????_??pC??a?"b??<Ό?????Z?X?g????????G???/>???? |???!&v?6??|&?T?s??C?? y??q??12??|???`???D?W8?w???Gx?c??Ӓ?=?W^'?w'S??]????A`?N??c?????)?}!80 ??I???c?b?:???????????S}?M?:??!??ǂşZ?\{?"h?????v??Y˱?^e~??4Q???>??? -?Z?s??S?~ç???Ӣ????_??li??{b ?????Ze???oO?:???????"]j%3?O??#4????W?G?g?O=?z??hU???g???h??hE@QOȚ ??k:???w'?????"u?˖?|?X??^^??`9?)?ߥ?1??ȣ?8???i?M=ҝ?#???>u?QS??㈑????n??l?fh? ? ??/?????q???h;gx?߮?????c?U?=???4z;-ʒ????????c1?c?倍??|m?????,?G???? ?(???J?c???&???e|,??%k{?3?O???o??????<v6? y???|???_??'.7?x?ҟ^??e???9?="" q?#m??y??ҟ~.?!?s?ş??ee??'rn="" ?????ş???c?]???Ա????,~??<?|?h?????~?{??x?DZ?<~?||??????כ??????g?fj?="" <????:6'????h??a????w??!?u?}`?k????q?߇?[y??fgӸ|="" ?h??o?"?~??<:'??????+i??l??\?fi?g<?(?c6?w???+?'?yٟ?(??,??n????'b??1y?="" '2??'??hװӋ??5`{?an??sn9??1??15??="v?ӎ?N??G?x从??쨃?O=j??S?v???N?z?" q??u?????찣Ù{???c?p?å????sg̷?,?i??g?v4??_??s??:<?k????="">????_?Xy??? ???^?݂~9!??8?rh? ?????> E??????2??ʬ:??f?۝ ??^C??z??(???M6c ?/?m????6#??Y?6#?X??p???r?f,??km???~f?>?:{?f???s???!?1????،5?|???k??X ?Wtl?B\?[??3??>gz??i???????a?ӱ޹z~??f???w??????3??Wn???ٌ??n????W?k_K gٌeX?Z}?zP?]գ}|l??/\w ???s????&s?ی??;?b???p?y?}٨?pn????a?+???e]?~(?i5?1,8, +??}e?????粖?(???? ?N?m??Yâ?s ?+?]?{Š?p?????Y ?e?+???{yG?}>?G??j??9?ఴ???????n???~??'??z??xf?ֿ|H?[5*|??ݟ ?Bp>c??qf?Ӄ??,?C??\???h???C????~?f?~П۫?Op???????7k]?+?_6???rzY1?t?t w~??b???? 8,?????}?6??ަ??Oqߥ[D?h??珥??p?&?}U?׀??}?v?a?}??ﰮ??@??9 GMp:{??r??uz<s??w??k??g?˧?e????&}_???{?v??6?? ?s??u?˓???w??g??̵n??nw?\?lҾ??\9?w?;?%???="" ?????]???y?kgn???z??&?ѯ?Ϝ???z="" ?ȏ?~??3?o??犟w?="" ?.?<???m????u??t??9k?????(???o????o?dɣ?="" ???dg??i.??="" ?g??r?߹]?g="" m?<????uyׯ???]gx??u??x??*?k?i?p~-?v????k?;?????^?t|??="" ?v8}???g???ż?q?i??u&?`d8="" ???͢??]^@???????????9]?cwם="M?&lt;?'?W?|GzX???._Vlp9?A?C?^0?K]??p:[???#?" k??="" ??????="{?ӑ??YC??R?S???}=??">???ֺ?? ??l??u??s]߯u???8??}??}??????Wl^?ڸ?v9?r???,? ???'??C?כuݙ[$?Wn?男?EpM-?"???e .?/?a????p??t ?Zڣ??.N??z?????5????j}??!??C?G>2??\?????;>??????O9|?G+?j?Ko???i??g??? 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X??^???G??|??0ٯ???V?????(o&????_?n,?? c~7n?3?uQ>??͟un???G'??z?|?oY?I?g??H?cuvă?8r>f˘????F??'?K\C?Sz???e?? ?Q?2?i???u??????̉?s??v??p\~6????G?5?V[~?t?|?i,??N?c?/q[,?S?=???~?x]k Oĵ??s??Q?Gz??#?"m?X?h?{?ִq???$??p?`?V???g???V??yn????a??{\^mux??O?{? 6&??[???G??v?˭$˜F)?|}?}?#G?3?q?W#?"?D??´1????,ɽhE9Z??$ϣ.#?ޱ??i?? ?6Bi?~?2?/?y?eA????{?\???N?z%?F?-ƍ?h??g?^???7D??c;?~??(????WGڋ8??~L? b??8?f??{]??E8DR^S??$?z?~?܋???}q?`?U'?b.?FG???K???C|^????ыr)??ܵ?rAm %?ao?}?g?ne{ :?|vc?M??g??? ?w??!ث??????????????6`???7??Y?nw9??j??A??O ???q?5???`?pUNh2??j?36aoDŽ?n ?No7?? ???8??kz~x???)?]O?????'?d?v> ???W;}???Ȼ???k?L??????_9џ???_?Ϯ?#??k???7?uߚ{?zڗքO?8?>????J_???N? M?~rx?[?=????^C????U?{,ɹ?c????߂/???3????S????h8?mx=>?q?|????w????x?? >?`r~??}?a?vu?&?e?g????&?]g=?V}?G?xxM ???(ca_Zk?<?N? Y??W????-<#???h????>???[???[?>?????{?F?s?o >j??W{?J_?֛???۩?Lu??}M???^Fj>??H?{? ?oX?t?? new-host:PhaseII ssshen$ head -n17 DK_A3_03.CEL ;={ffymetrix-calvin- intensity60000029318-1257442883-0000021238-0000007719-0000000038en-US +affymetrix-algorithm-nameDFeature Extraction Cell Generation text/plainaffymetrix-algorithm-version1.0.0.676 text/plainaffymetrix-array-type?MoGene-1_0-st-v1 text/plainaffymetrix-library-package?Universal text/plainaffymetrix-cel-rowstext/x-calvin-integer-32affymetrix-cel- colstext/x-calvin-integer-32program-company Affymetrix, Inc. text/plain program-nameFAffymetrix Genechip Command Console text/plain program-id0.0.0.676 text/plain,affymetrix-algorithm-param-FeatureExtractioTRUE text/plain1affymetrix-algorithm-param-IgnoreShiftRowOutliers FALSE text/plain(affymetrix-algorithm-param-FixedCellSizTRUE text/plain&affymetrix-algorithm-param-UseSubgridTRUE text/plain*affymetrix-algorithm-param-RandomizePixels FALSE text/plain%affymetrix-algorithm-param-ErrorBasisStdvMean text/plain+affymetrix-algorithm-param-PercentileSpreadAptext/x-calvin- float"affymetrix-algorithm-param-StdMult??text/x-calvin-float *affymetrix-algorithm-param-ExtendPoolWidthtext/x-calvin-integer-32 +affymetrix-algorithm-param-ExtendPoolHeighttext/x-calvin-integer-32 %affymetrix-algorithm-param-OutlierLow???text/x-calvin-float &affymetrix-algorithm-param-OutlierHigh??text/x-calvin- float4affymetrix-algorithm-param-OutlierRatioLowPercentile7text/x -calvin-integer-325affymetrix-algorithm-param- OutlierRatioHighPercentileKtext/x-calvin-integer-32%affymetrix- algorithm-param-CellMargintext/x-calvin-integer-32.affymetrix- algorithm-param-HalfCellRowsDivisortext/x-calvin-integer- 320affymetrix-algorithm-param-HalfCellRowsRemaindertext/x-calvin- integer-327affymetrix-algorithm-param- CellIntensityCalculationTypePercentile new-host:PhaseII ssshen$ On Mon, Mar 8, 2010 at 2:46 PM, cstrato <cstrato@aon.at> wrote: > Dear Steve, > > As you have mentioned in your last mail, you got a corrupt CEL-file which > has a size of more than 10-times the usual size. This could be a missing > EOF. > However, the error message you get should only appear for Version=3 > CEL-files, i.e. text files, which could explain the large size. Could it be > that someone has converted this CEL-file from binary to text format? > > Could you please run the following commands: > $ head -n17 DK_A1_01.CEL > $ head -n17 DK_A3_03.CEL > and send me the output. > > Best regards > Christian > > > Steve Shen wrote: > >> The problem is indeed this CEL file. It went well if I remove this .CEL >> file from import list. The question is what's wrong with this file. It can >> be read as normal one from affy tools (e.g. expression console). If someone >> interested in this problem, I can attached both good and bad cel files. >> >> Thanks, >> Steve >> >> On Sun, Mar 7, 2010 at 10:00 PM, Steve Shen <sshen@bu.edu <mailto:="">> sshen@bu.edu>> wrote: >> >> The problem seems to related to one of the cel files, error says: >> >> Error: Header line of file >> <~/Projects/DKotton_Gustavo/PhaseII/DK_A1_01.CEL> is not correct. >> What does this mean? To me all .cel files are same. >> >> Best, >> Steve >> >> >> >> On Sun, Mar 7, 2010 at 9:51 PM, Steve Shen <sshen@bu.edu>> <mailto:sshen@bu.edu>> wrote: >> >> Sorry, misclick! >> >> On Sun, Mar 7, 2010 at 9:46 PM, Steve Shen <sshen@bu.edu>> <mailto:sshen@bu.edu>> wrote: >> >> Dear Christian, >> >> Just couldn't figure out what exactly problem is, but >> maybe you can point out easily. I have a set of cel files >> which derived from two different batches. I tried to >> import data with one command line, but it didn't work (the >> error message is below) and getTreeNames give me an error >> says "object 'xxx.root' not found", but root file is >> actually in the folder. >> >> I then import first batch cel files first and use addData >> command to import second batch. It turned out that the >> importdata command worked well as expected, but addData >> command generated same exact error message as first time >> (see below). However, this time the getTreeNames worked. >> >> The commands and errors are appended. Thanks, >> >> Steve >> >> >> ###import two batches >> >> >> > data.xps <- import.data(scheme.mogene10st, >> "gm_dk_phase2", filedir = datdir, celfiles= celfiles, >> celnames=celnames) >> >> Errors, (see below) >> > getTreeNames(rootFile(data.xps)) >> Error: object 'data.xps' not found >> Error in rootFile(data.xps) : >> error in evaluating the argument 'object' in selecting a >> method for function 'rootFile' >> >> ###import first batch first, then add >> > data.gm.dk.xps <- import.data(scheme.mogene10st, >> "gm_dk_phase2", filedir=datdir, celdir=celdir, >> celfiles=celfiles, celnames=celnames) >> #no errors >> > data.gm.dk.xps <- addData(data.gm.dk.xps, celdir=celdir, >> celfiles=celfiles02, celnames=celnames02) >> Error in .local(object, ...) : error in function ‘ImportData’ >> Opening file <~/XPS/scheme/Scheme_MoGene10stv1r4_na30.root> in >> <read> mode... >> Opening file <~/XPS/ROOTdata/gm_dk_phase2_cel.root> in >> <update> mode... >> Importing <~/Projects/DKotton_Gustavo/PhaseII/DK_A7_07.CEL> as >> <dk_a7_07.cel>... >> hybridization statistics: >> 1 cells with minimal intensity 18 >> 1 cells with maximal intensity 11987 >> Importing <~/Projects/DKotton_Gustavo/PhaseII/DK_A8_08.CEL> as >> <dk_a8_08.cel>... >> hybridization statistics: >> 17 cells with minimal intensity 21 >> 1 cells with maximal intensity 13337 >> Importing <~/DKotton_Gustavo/PhaseII/DK_B1_09.CEL> as >> <dk_b1_09.cel>... >> hybridization statistics: >> 2 cells with minimal intensity 19 >> 1 cells with maximal intensity 11798 >> Importing <~/Projects/DKotton_Gustavo/PhaseII/DK_A4_04.CEL> as >> <dk_a4_04.cel>... >> hybridization statistics: >> 27 cells with minimal intensity 19 >> 1 cells with maximal intensity 14787 >> Importing <~/Projects/DKotton_Gustavo/PhaseII/DK_A5_05.CEL> as >> <dk_a5_05.cel>... >> Error: Header line of file >> >> </users> >> is not correct. >> hybridization statistics: >> 7 cells with minimal intensity 20 >> 1 cells with maximal intensity 15474 >> Importing <~/Projects/DKotton_Gustavo/PhaseII/DK_A3_03.CEL> as >> <dk_a3_03.cel>... >> hybridization statistics: >> 1 cells with minimal intensity 20 >> 1 cells with maximal intensity 12507 >> >> >> >> > [[alternative HTML version deleted]]
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Dear Steve, Currently, CEL-files can exist in three formats, .i.e text, xda and calvin, where both xda and calvin are binary formats, however both have header lines which are text only. Your output for DK_A3_03.CEL shows the header of a calvin file. In contrast, the output for DK_A1_01.CEL is binary only, thus the complete header is missing. I cannot even say that this is a CEL-file at all. I am afraid that you cannot use this CEL-file. If you have access to the DK_A1_01.DAT file you should be able recreate the corresponding CEL- file. Best regards Christian Steve Shen wrote: > Hi Christian, > > It's possible. I looked the time stamp for the files that bad one has > different time stamp too. Here is what I got after command issued. > > Best, > Steve > > ew-host:PhaseII ssshen$ head -n17 DK_A1_01.CEL > ?0?K???UU?>??3??b???dd?D?**??7QQ? > ??hXd7???"""?M??LoD?97##3?9f??s3?!????cL95N}?? SOx?+-_??cg?????????;?|???#?y?????:?H;???z??}t??v??Gf??'v???N]t?)???z? > N???????/yR???zq??=??O? ?N9i??????'?|?I'/:??SOZtz??( > ???q??;???q?aS;X?v??????^?????b???)v??l????k;?N > > ?;???[d??I?8??8[h????E? |{p??8?????????i?'X?p?>??'?+O???w > ??Z? > >??"~o?K?? ??P > ;.|??'??? > ?zj???v?b??:???~????S???????7?k?S?^Ozgx????????????? > ??????.??Be??~o??w;l???)???????=6????>?n?k6?Y????1w?U??y????????v??g p?I?z???}\?|???????? ]???'??!3???1?/?N??=kG???$?Y??7N????{??e??d~B?????wo > ;.?jy\????/??Z?7,????xc???????s????d????????>?g???4?=????~??|zEM??g? O?'%-?~=???*??6>?q>y??t ???-?G???F??X??^????? > ??Z ?=A+|?????M9Fl???????+;?e?C ?i??5? > Y??-?1?6?~?y????^???i0j???w????=?:?q?jqbZ?.-i??DK?_?S??u????|C??}??? IOL??b??~??K?y???'????? > ?A?O?????!?W2???????+/xB??~;-|s?????!???.(??????????;??Qv??hE??{?[?o > Zm.V??y?rg????x?`Q?G???*???E??N?xh???*??*??o?"????U?8?T???????33??>* > ?h??Z?????>??V??>???c?'????q???????Os????#k??? ~????>?x??|???????A???Q??z_~?G???kN?l?X > ?0p???????????_??pC??a?"b?????? > > |???!&v?6??|&?T?s??C?? > y??q??12??|???`???D?W8?w???Gx?c????=?W^'?w'S??]????A`?N??c?????)?}!8 0??I???c?b?:???????????S}?M?:??!????Z?\{?"h?????v??Y??^e~??4Q???>???-? Z?s??S?~?????????_??li??{b > > ?????Ze???oO?:???????"]j%3?O??#4????W?G?g?O=?z??hU???g???h??hE at QO???k:???w'?????"u? ??*E!8<v?_?p??w? q?????=""> {?? > :5????>??|?X??^^??`9?)???1????8???i?M=??#???>u?QS???????n??l?fh?? > > ??/?????q???h;gx???????c?U?=???4z;-?????????c1?c????|m?????,?G????? > (??? > J?c???&???e|,??%k{?3?O???o??????<v6? y???|???_??'.7?x??^??e???9?q?#m="" ??y???~.?!?s????ee??'rn=""> > ?????????c?]????????,~?? > ?H??O?"?~??<:'??????+i??L??\?FI?G '2??'??H????5`{?an??SN9??1??15??=v???N??G?x?????O=j??S?v???N?z?Q?? > u????? ??{???c?p??????Sg??,?i??G?v4??_??S??:????_?Xy??????^? > ?~9!??8?rh? > ?????> > E??????2???:??f?? > ??^C??z??(???M6c > ?/?m????6#??Y?6#?X??p???r?f,??km???~f?>?:{?f???s???!?1?????5?|???k?? X?Wtl?B\?[??3??>gz??i???????a???z~??f???w??????3??Wn??????n????W?k_Kg? eX?Z}?zP?]?}|l??/\w > ???s????&s????;?b???p?y?}??pn????a?+???e]?~(?i5?1,8, > +??}e???????(???? ?N?m??Y??s > ?+?]?{??p?????Y > > ?e?+???{yG?}>?G??j??9?????????n? ?????]?B?]?1????~??m?t?u?j??O??????It????:W?u|n?}??????1??/?????U??? > > ???????D???]??-?7?}???V?meK?h}???????t???>??~??'??z??xf??|H?[5*|???? Bp>c??qf????,?C??\???h???C????~?f?~???Op???????7k]?+?_6???rzY1?t?tw~?? b???? > 8,?????}?6?????Oq?[D?h?????p?&?}U????}?v?a?}?????@??9 > > GMp:{??r??uz<s??w??k??g???e????&}_???{?v??6??> ?s??u?????w??G???N??Nw?\?l???\9?W?;?%??? > > ?????]???Y?kgn???Z??&???????z ???~??3?O???W?/?.? 9K?????(???o????o?D?? > > ???Dg??i.?? > /?g??R??]?G > M? ?V8}???g?????q?I??U&?`D8 > ??????]^@???????????9]?cW?=M? ??????={????YC??R?S???}=??>?????? > ??l??u??s]?u???8??}??}??????Wl^???v9?r???,? > ???'??C??u?[$?Wn???EpM-?" ~??????]???????en????t:??]?????GM? ??g?:>???e > .?/?a????p??t > ?Z???.N??z?????5????j}??!??C?G>2??\?????;>??????O9|?G+?j?Ko???i??g??? > D??t?3??????l??W??=????n?}tD???p??]/?????<c?g????m????>??x.?@?3?@?_?? > z>?7??^??G?.??._>8???l?c?;?c????G??k ?5???s??G?.a?D> > ?8?/u9p??CI?w?g????gG????KT6?????l?????K?_4,?,u?$?-??=?p???w????|?=n ?t???/?<$?D;??t?????s{?? > K?O???;]t??G??9g??=?????>?T}~???>>?o??&???? > > ?$?9??_??????l????q_?j?k??????3?n??g??7????n??g????Y?^???????????>?w c?? > r8???t???<f????| ???)c???:?="">Ir?????W?K??m?5??D???Y?????8??{_?{??? > O?{?w?s???1???! > > ?????????z??9c?k??q?i.?l?????s????G????}c??7??7????"??k??1?m?i???~?? s?g??? > 8?'????o'?g?? g?#~??k??e,/?8??&??'X??????3??Y?t?f????y4?57???)?eY?E????5?q???1k?0? 9??`?- > zh > > ???4??????dY??+??c???>????x?d?~?6????????}????{??H{S-??????cI????y?p \???? > C??.{??{??gL?5nY??(wkm|???M?e??k?w{??#\??6c??????< > ?I??#?y??????8?:?lG9??L???=???z%???O?? > > X??^???G??|??0????V?????(o&????_?n,?? > c~7n?3?uQ>???un???G'??z?|?oY?I?g??H?cuv??8r>f?????F??'?K\C?Sz???e??? Q?2?i???u????????s??v??p\~6????G?5?V[~?t?|?i,??N?c?/q[,?S?=???~?x]k > > O???s??Q?Gz??#?"m?X?h?{??q???$??p?`?V???g???V??yn????a??{\^mux??O?{? 6&??[???G??v??$?F)?|}?}?#G?3?q?W#?"?D???1????,?hE9Z??$?.#????i???6Bi?~ ?2?/?y?eA????{?\???N?z%?F?-??h??g?^???7D??c;?~??(????WG?8??~L?b??8?f?? {]??E8DR^S??$?z?~?????}q?`?U'?b.?FG???K???C|^?????r)????rAm%?ao?}?g?ne { > :?|vc?M??g??? > ?w??!???????????????6`???7??Y?nw9??j??A??O > ???q?5???`?pUNh2??j?36ao??n ?No7?? ???8??kz~x???)?]O?????'?d?v> > ???W;}???????k?L??????_9????_???#??k???7?u?{?z??O?8?>????J_???N?M?~r x?[?=????^C????U?{,??c?????/???3????S????h8?mx=>?q?|????w????x??>?`r~? ?}?a?vu?&?e?g????&?]g=?V}?G?xxM > > ???(ca_Zk?<?N? > Y??W????-<#???h????>???[???[?>?????{?F?s?o > >j??W{?J_???????Lu??}M???^Fj>??H?{? ?oX?t?? > > > > new-host:PhaseII ssshen$ head -n17 DK_A3_03.CEL > ;={ffymetrix-calvin- intensity60000029318-1257442883-0000021238-0000007719-0000000038en-US +affymetrix-algorithm-nameDFeature > Extraction Cell Generation > text/plainaffymetrix-algorithm-version1.0.0.676 > text/plainaffymetrix-array-type?MoGene-1_0-st-v1 > text/plainaffymetrix-library-package?Universal > text/plainaffymetrix-cel-rowstext/x-calvin-integer-32affymetrix-cel- colstext/x-calvin-integer-32program-company > Affymetrix, Inc. > text/plain > program-nameFAffymetrix Genechip Command Console > text/plain > program-id0.0.0.676 > text/plain,affymetrix-algorithm-param-FeatureExtractioTRUE > text/plain1affymetrix-algorithm-param-IgnoreShiftRowOutliers > FALSE > text/plain(affymetrix-algorithm-param-FixedCellSizTRUE > text/plain&affymetrix-algorithm-param-UseSubgridTRUE > text/plain*affymetrix-algorithm-param-RandomizePixels > FALSE > text/plain%affymetrix-algorithm-param-ErrorBasisStdvMean > text/plain+affymetrix-algorithm-param-PercentileSpreadAptext/x -calvin-float"affymetrix-algorithm-param-StdMult??text/x-calvin-float *affymetrix-algorithm-param-ExtendPoolWidthtext/x-calvin-integer-32 +affymetrix-algorithm-param-ExtendPoolHeighttext/x-calvin-integer-32 %affymetrix-algorithm-param-OutlierLow???text/x-calvin-float &affymetrix-algorithm-param-OutlierHigh??text/x-calvin- float4affymetrix-algorithm-param-OutlierRatioLowPercentile7text/x -calvin-integer-325affymetrix-algorithm-param- OutlierRatioHighPercentileKtext/x-calvin-integer-32%affymetrix- algorithm-param-CellMargintext/x-calvin-integer-32.affymetrix- algorithm-param-HalfCellRowsDivisortext/x-calvin-integer- 320affymetrix-algorithm-param-HalfCellRowsRemaindertext/x-calvin- integer-327affymetrix-algorithm-param- CellIntensityCalculationTypePercentile > new-host:PhaseII ssshen$ > > > On Mon, Mar 8, 2010 at 2:46 PM, cstrato <cstrato at="" aon.at=""> <mailto:cstrato at="" aon.at="">> wrote: > > Dear Steve, > > As you have mentioned in your last mail, you got a corrupt > CEL-file which has a size of more than 10-times the usual size. > This could be a missing EOF. > However, the error message you get should only appear for > Version=3 CEL-files, i.e. text files, which could explain the > large size. Could it be that someone has converted this CEL-file > from binary to text format? > > Could you please run the following commands: > $ head -n17 DK_A1_01.CEL > $ head -n17 DK_A3_03.CEL > and send me the output. > > Best regards > Christian > > > Steve Shen wrote: > > The problem is indeed this CEL file. It went well if I remove > this .CEL file from import list. The question is what's wrong > with this file. It can be read as normal one from affy tools > (e.g. expression console). If someone interested in this > problem, I can attached both good and bad cel files. > > Thanks, > Steve > > On Sun, Mar 7, 2010 at 10:00 PM, Steve Shen <sshen at="" bu.edu=""> <mailto:sshen at="" bu.edu=""> <mailto:sshen at="" bu.edu=""> <mailto:sshen at="" bu.edu="">>> wrote: > > The problem seems to related to one of the cel files, error > says: > > Error: Header line of file > <~/Projects/DKotton_Gustavo/PhaseII/DK_A1_01.CEL> is not > correct. > What does this mean? To me all .cel files are same. > > Best, > Steve > > > > On Sun, Mar 7, 2010 at 9:51 PM, Steve Shen <sshen at="" bu.edu=""> <mailto:sshen at="" bu.edu=""> > <mailto:sshen at="" bu.edu="" <mailto:sshen="" at="" bu.edu="">>> wrote: > > Sorry, misclick! > > On Sun, Mar 7, 2010 at 9:46 PM, Steve Shen > <sshen at="" bu.edu="" <mailto:sshen="" at="" bu.edu=""> > <mailto:sshen at="" bu.edu="" <mailto:sshen="" at="" bu.edu="">>> wrote: > > Dear Christian, > > Just couldn't figure out what exactly problem is, but > maybe you can point out easily. I have a set of cel > files > which derived from two different batches. I tried to > import data with one command line, but it didn't > work (the > error message is below) and getTreeNames give me an > error > says "object 'xxx.root' not found", but root file is > actually in the folder. > > I then import first batch cel files first and use > addData > command to import second batch. It turned out that the > importdata command worked well as expected, but addData > command generated same exact error message as first > time > (see below). However, this time the getTreeNames > worked. > > The commands and errors are appended. Thanks, > > Steve > > > ###import two batches > > > > data.xps <- import.data(scheme.mogene10st, > "gm_dk_phase2", filedir = datdir, celfiles= celfiles, > celnames=celnames) > > Errors, (see below) > > getTreeNames(rootFile(data.xps)) > Error: object 'data.xps' not found > Error in rootFile(data.xps) : > error in evaluating the argument 'object' in selecting a > method for function 'rootFile' > > ###import first batch first, then add > > data.gm.dk.xps <- import.data(scheme.mogene10st, > "gm_dk_phase2", filedir=datdir, celdir=celdir, > celfiles=celfiles, celnames=celnames) > #no errors > > data.gm.dk.xps <- addData(data.gm.dk.xps, celdir=celdir, > celfiles=celfiles02, celnames=celnames02) > Error in .local(object, ...) : error in function > ?ImportData? > Opening file > <~/XPS/scheme/Scheme_MoGene10stv1r4_na30.root> in > <read> mode... > Opening file <~/XPS/ROOTdata/gm_dk_phase2_cel.root> in > <update> mode... > Importing > <~/Projects/DKotton_Gustavo/PhaseII/DK_A7_07.CEL> as > <dk_a7_07.cel>... > hybridization statistics: > 1 cells with minimal intensity 18 > 1 cells with maximal intensity 11987 > Importing > <~/Projects/DKotton_Gustavo/PhaseII/DK_A8_08.CEL> as > <dk_a8_08.cel>... > hybridization statistics: > 17 cells with minimal intensity 21 > 1 cells with maximal intensity 13337 > Importing <~/DKotton_Gustavo/PhaseII/DK_B1_09.CEL> as > <dk_b1_09.cel>... > hybridization statistics: > 2 cells with minimal intensity 19 > 1 cells with maximal intensity 11798 > Importing > <~/Projects/DKotton_Gustavo/PhaseII/DK_A4_04.CEL> as > <dk_a4_04.cel>... > hybridization statistics: > 27 cells with minimal intensity 19 > 1 cells with maximal intensity 14787 > Importing > <~/Projects/DKotton_Gustavo/PhaseII/DK_A5_05.CEL> as > <dk_a5_05.cel>... > Error: Header line of file > > </users> > is not correct. > hybridization statistics: > 7 cells with minimal intensity 20 > 1 cells with maximal intensity 15474 > Importing > <~/Projects/DKotton_Gustavo/PhaseII/DK_A3_03.CEL> as > <dk_a3_03.cel>... > hybridization statistics: > 1 cells with minimal intensity 20 > 1 cells with maximal intensity 12507 > > > > >
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