Can you tell me if these are real Excel files or just text files with a .xls extension? -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Srinivas Iyyer Sent: 29 September 2005 00:00 To: bioconductor at stat.math.ethz.ch Subject: [BioC] problem reading GenePix files with .XLS extension Hello: I am a fist time trying to analyze cdna data and right at the first step i was bombed. can any one please help me: >library(Biobase) >library(marray) >samples = read.phenoData("phenodata.txt",header=TRUE, as.is = TRUE) > files = samples$fileName spree of errors starts here: ## the .XLS files are downloaded from Garber_lung data. ## software used in GenePix ## path : I am using windows based R so changed the ## directory to where all my .XLS files area locatd > mdata = read.GenePix(files, path=".") Error in if (skip > 0) readLines(file, skip) : missing value where TRUE/FALSE needed >mdata = read.GenePix(files, ext = 'xls') Error in if (skip > 0) readLines(file, skip) : missing value where TRUE/FALSE needed > mdata = read.marrayRaw(files,ext = "xls") Error in if is.na(pattern)) { : argument is of length zero > nmdata = read.marrayRaw(nfs, ext="xls") Error in if is.na(pattern)) { : argument is of length zero > nmdata = read.marrayRaw(nfs, ext="xls", skip = 22) Reading ... ./shu058.248-97_LCLC.xls Error in read.table(f, skip = skip2, header = TRUE, sep = sep, quote = quote, : unused argument(s) (ext ...) How do I read these XLS files and retain all the inforamtion. can any one please give R commands till I get to normalization procedure. Thank you srini _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor

this is Garber lung data. there are 73 files. they all have this.xls extension and have the following content. !Exptid=5715 !Experiment Name=58-95_SCC !Organism=Homo sapiens !Category=Primary tumor !Subcategory=Lung Cancer !Description=mRNA from I. Petersen. Total RNA isloted with Trizol. mRNA isolated with Invitrogen isolation kit. Hyb by M. Garber. !Experimenter=Mitchell Garber !Contact email=garber at genome.stanford.edu !Contact Address1=Genetics !Contact Address2=L-311 !SlideName=shac046 !Printname=SHAC2 !Tip Configuration=Standard 32-tip !Columns per Sector=28 !Rows per Sector=27 !Column Spacing=175 !Row Spacing=175 !Channel 1 Description=CRE reference !Channel 2 Description=58-95_SCC !Scanning Software=GenePix !Software version=2.0.1.19 !Scanning parameters= SPOT NAME Clone ID Gene Symbol Gene Name Cluster ID Accession Preferred name CH1D_MEDIAN CH1I_MEDIAN CH1_PER_SAT CH1I_SD CH1B_MEAN CH1B_MEDIAN CH1B_SD CH1D_MEAN CH2I_MEAN CH2D_MEAN CH2D_MEDIAN CH2I_MEDIAN CH2_PER_SAT CH2I_SD CH2B_MEAN CH2B_MEDIAN CH2B_SD CH2BN_MEDIAN CH2DN_MEAN CH2IN_MEAN CH2DN_MEDIAN CH2IN_MEDIAN CORR DIAMETER FLAG LOG_RAT2N_MEAN LOG_RAT2N_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN PERGTBCH1I_1SD PERGTBCH1I_2SD PERGTBCH2I_1SD PERGTBCH2I_2SD RAT1_MEAN RAT1N_MEAN RAT2_MEAN RAT2_MEDIAN RAT2_SD RAT2N_MEAN RAT2N_MEDIAN REGR SUM_MEAN SUM_MEDIAN TOT_BPIX TOT_SPIX X_COORD Y_COORD TOP BOT LEFT RIGHT SECTOR SECTORROW SECTORCOL SOURCE PLATE PROW PCOL FAILED IS_VERIFIED IS_CONTAMINATED LUID 1 13762 IMAGE:753234 ZFX **zinc finger protein, X-linked Hs.2074 AA406372 121 116 475 1092 732 389 360 330 672 1002 .85 0 .5 1.499 88 80 .649 .707 1.541 1.415 1.515 511 120 67 79 35 47 1 1 1 GF200:96(1A1):384(1A1) 3 A 1 0 Y U 500001 2 13766 IMAGE:50794 ZNF133 zinc finger protein 133 (clone pHZ-13) Hs.78434 H17047 123 118 620 771 390 404 381 350 358 708 .78 0 -.792 .714 77 64 1.59 1.732 .629 .577 .579 346 120 66 78 51 63 1 1 2 GF200:96(1A3):384(1A5) 3 A 5 0 Y U 500003 3 13770 IMAGE:302190 MLLT2 **myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 2 Hs.114765 N77807 131 122 440 563 194 390 369 339 178 517 .49 0 -1.305 .535 79 43 2.268 2.471 .441 .405 .406 333 120 66 78 65 77 1 1 3 GF200:96(1A5):384(1A9) 3 A 9 0 Y U 500005 --- "michael watson (IAH-C)" <michael.watson at="" bbsrc.ac.uk=""> wrote: > Can you tell me if these are real Excel files or > just text files with a > .xls extension? > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On > Behalf Of Srinivas > Iyyer > Sent: 29 September 2005 00:00 > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] problem reading GenePix files with > .XLS extension > > Hello: > > > I am a fist time trying to analyze cdna data and > right at the first step > i was bombed. can any one please help me: > > > >library(Biobase) > >library(marray) > >samples = > read.phenoData("phenodata.txt",header=TRUE, > as.is = TRUE) > > files = samples$fileName > > spree of errors starts here: > > ## the .XLS files are downloaded from Garber_lung > data. > ## software used in GenePix > ## path : I am using windows based R so changed the > ## directory to > where all my .XLS files area locatd > > > mdata = read.GenePix(files, path=".") > Error in if (skip > 0) readLines(file, skip) : > missing value where TRUE/FALSE needed > > > >mdata = read.GenePix(files, ext = 'xls') > Error in if (skip > 0) readLines(file, skip) : > missing value where TRUE/FALSE needed > > > > mdata = read.marrayRaw(files,ext = "xls") > Error in if is.na(pattern)) { : argument is of > length zero > > > nmdata = read.marrayRaw(nfs, ext="xls") > Error in if is.na(pattern)) { : argument is of > length zero > > nmdata = read.marrayRaw(nfs, ext="xls", skip = 22) > Reading ... ./shu058.248-97_LCLC.xls > Error in read.table(f, skip = skip2, header = TRUE, > sep = sep, quote = > quote, : > unused argument(s) (ext ...) > > > How do I read these XLS files and retain all the > inforamtion. > > can any one please give R commands till I get to > normalization procedure. > > Thank you > > srini > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > >