GCRMA Error
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@denise-mauldin-3688
Last seen 10.2 years ago
Greetings all, I'm running gcrma on arrays from GSE9171 and I'm getting the infamous 'NAs are not allowed in subscripted assignments' error. > GSE9171_GPL570_gcrma <- gcrma(GSE9171_GPL570) Adjusting for optical effect..............................Done. Computing affinities.Error in tmp.exprs[pmIndex[subIndex]] = apm : NAs are not allowed in subscripted assignments > traceback() 3: compute.affinities(cdfName(object), verbose = verbose) 2: bg.adjust.gcrma(object, affinity.info = affinity.info, affinity.source = affinity.source, NCprobe = NCprobe, type = type, k = k, stretch = stretch, correction = correction, GSB.adjust = GSB.adjust, rho = rho, optical.correct = optical.correct, verbose = verbose, fast = fast) 1: gcrma(GSE9171_GPL570) > compute.affinities(cdfname="HGU133Plus2_Hs_ENTREZG", verbose=TRUE) Computing affinities.Error in tmp.exprs[pmIndex[subIndex]] = apm : NAs are not allowed in subscripted assignments Is this an error in the HGU133Plus2_Hs_ENTREZG CDF from brainarray? Is there something I can do to fix this? Thanks, Denise > sessionInfo() R version 2.9.1 (2009-06-26) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] hgu133plus2hsentrezgprobe_12.0.0 AnnotationDbi_1.6.1 [3] hgu133plus2hsentrezgcdf_11.0.1 gcrma_2.16.0 [5] Biostrings_2.12.10 IRanges_1.2.3 [7] limma_2.18.3 affy_1.22.1 [9] Biobase_2.4.1 loaded via a namespace (and not attached): [1] affyio_1.12.0 DBI_0.2-4 preprocessCore_1.6.0 [4] RSQLite_0.7-3 splines_2.9.1 tools_2.9.1
cdf gcrma cdf gcrma • 2.1k views
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Zhijin Wu ▴ 260
@zhijin-wu-2378
Last seen 10.2 years ago
Hi Denise I'll download the dataset and try to reproduce the error first and get back to you Jean Denise Mauldin wrote: > Greetings all, > > I'm running gcrma on arrays from GSE9171 and I'm getting the infamous > 'NAs are not allowed in subscripted assignments' error. > > >> GSE9171_GPL570_gcrma <- gcrma(GSE9171_GPL570) >> > Adjusting for optical effect..............................Done. > Computing affinities.Error in tmp.exprs[pmIndex[subIndex]] = apm : > NAs are not allowed in subscripted assignments > >> traceback() >> > 3: compute.affinities(cdfName(object), verbose = verbose) > 2: bg.adjust.gcrma(object, affinity.info = affinity.info, > affinity.source = affinity.source, > NCprobe = NCprobe, type = type, k = k, stretch = stretch, > correction = correction, GSB.adjust = GSB.adjust, rho = rho, > optical.correct = optical.correct, verbose = verbose, fast = fast) > 1: gcrma(GSE9171_GPL570) > >> compute.affinities(cdfname="HGU133Plus2_Hs_ENTREZG", verbose=TRUE) >> > Computing affinities.Error in tmp.exprs[pmIndex[subIndex]] = apm : > NAs are not allowed in subscripted assignments > > Is this an error in the HGU133Plus2_Hs_ENTREZG CDF from brainarray? > Is there something I can do to fix this? > > Thanks, > Denise > > >> sessionInfo() >> > R version 2.9.1 (2009-06-26) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDEN TIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] hgu133plus2hsentrezgprobe_12.0.0 AnnotationDbi_1.6.1 > [3] hgu133plus2hsentrezgcdf_11.0.1 gcrma_2.16.0 > [5] Biostrings_2.12.10 IRanges_1.2.3 > [7] limma_2.18.3 affy_1.22.1 > [9] Biobase_2.4.1 > > loaded via a namespace (and not attached): > [1] affyio_1.12.0 DBI_0.2-4 preprocessCore_1.6.0 > [4] RSQLite_0.7-3 splines_2.9.1 tools_2.9.1 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- ------------------------------------------- Zhijin (Jean) Wu Assistant Professor of Biostatistics Brown University, Box G-S121 Providence, RI 02912 Tel: 401 863 1230 Fax: 401 863 9182 http://www.stat.brown.edu/zwu
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I am often using the combination of GCRMA and the remapped CDFs from the Brainarray group for various arrays, and never got a problem... So I downloaded the first three cel files from GSE9171 (GSM231709.CEL, GSM231712.CEL, GSM231715.CEL), ran GCRMA, and indeed everything goes fine. Please note that I use a different name for the CDF than you do; I don't know whether this may cause your problem? In my case the CDF and probe file are automatically downloaded from the BioC repository. HTH, Guido > library(affy) > library(gcrma) > > affy.data <- ReadAffy(cdfname="hgu133plus2hsentrezg") > > x.norm <- gcrma(affy.data) Adjusting for optical effect......Done. Computing affinitiesLoading required package: AnnotationDbi .Done. Adjusting for non-specific binding......Done. Normalizing Calculating Expression > > affy.data AffyBatch object size of arrays=1164x1164 features (8 kb) cdf=hgu133plus2hsentrezg (17788 affyids) number of samples=6 number of genes=17788 annotation=hgu133plus2hsentrezg notes= > x.norm ExpressionSet (storageMode: lockedEnvironment) assayData: 17788 features, 3 samples element names: exprs phenoData sampleNames: GSM231709.CEL, GSM231712.CEL, GSM231715.CEL (3 total) varLabels and varMetadata description: sample: arbitrary numbering featureData featureNames: 1_at, 10_at, ..., AFFX-TrpnX-M_at (17788 total) fvarLabels and fvarMetadata description: none experimentData: use 'experimentData(object)' Annotation: hgu133plus2hsentrezg > sessionInfo() R version 2.9.0 (2009-04-17) i386-pc-mingw32 locale: LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] hgu133plus2hsentrezgprobe_12.0.0 AnnotationDbi_1.6.1 [3] hgu133plus2hsentrezgcdf_12.0.0 gcrma_2.16.0 [5] Biostrings_2.12.9 IRanges_1.2.3 [7] affy_1.22.1 Biobase_2.4.1 loaded via a namespace (and not attached): [1] affyio_1.12.0 DBI_0.2-4 preprocessCore_1.6.0 [4] RSQLite_0.7-1 splines_2.9.0 tools_2.9.0 > ------------------------------------------------ Guido Hooiveld, PhD Nutrition, Metabolism & Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 internet: http://nutrigene.4t.com email: guido.hooiveld at wur.nl > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Zhijin Wu > Sent: 17 November 2009 05:58 > To: Denise Mauldin > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] GCRMA Error > > Hi Denise > > I'll download the dataset and try to reproduce the error > first and get back to you > > Jean > > Denise Mauldin wrote: > > Greetings all, > > > > I'm running gcrma on arrays from GSE9171 and I'm getting > the infamous > > 'NAs are not allowed in subscripted assignments' error. > > > > > >> GSE9171_GPL570_gcrma <- gcrma(GSE9171_GPL570) > >> > > Adjusting for optical effect..............................Done. > > Computing affinities.Error in tmp.exprs[pmIndex[subIndex]] = apm : > > NAs are not allowed in subscripted assignments > > > >> traceback() > >> > > 3: compute.affinities(cdfName(object), verbose = verbose) > > 2: bg.adjust.gcrma(object, affinity.info = affinity.info, > > affinity.source = affinity.source, > > NCprobe = NCprobe, type = type, k = k, stretch = stretch, > > correction = correction, GSB.adjust = GSB.adjust, rho = rho, > > optical.correct = optical.correct, verbose = verbose, fast = > > fast) > > 1: gcrma(GSE9171_GPL570) > > > >> compute.affinities(cdfname="HGU133Plus2_Hs_ENTREZG", verbose=TRUE) > >> > > Computing affinities.Error in tmp.exprs[pmIndex[subIndex]] = apm : > > NAs are not allowed in subscripted assignments > > > > Is this an error in the HGU133Plus2_Hs_ENTREZG CDF from brainarray? > > Is there something I can do to fix this? > > > > Thanks, > > Denise > > > > > >> sessionInfo() > >> > > R version 2.9.1 (2009-06-26) > > x86_64-unknown-linux-gnu > > > > locale: > > > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US > > > .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N > > > AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI > > FICATION=C > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] hgu133plus2hsentrezgprobe_12.0.0 AnnotationDbi_1.6.1 > > [3] hgu133plus2hsentrezgcdf_11.0.1 gcrma_2.16.0 > > [5] Biostrings_2.12.10 IRanges_1.2.3 > > [7] limma_2.18.3 affy_1.22.1 > > [9] Biobase_2.4.1 > > > > loaded via a namespace (and not attached): > > [1] affyio_1.12.0 DBI_0.2-4 preprocessCore_1.6.0 > > [4] RSQLite_0.7-3 splines_2.9.1 tools_2.9.1 > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > -- > ------------------------------------------- > Zhijin (Jean) Wu > Assistant Professor of Biostatistics > Brown University, Box G-S121 > Providence, RI 02912 > > Tel: 401 863 1230 > Fax: 401 863 9182 > http://www.stat.brown.edu/zwu > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > >
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Hi again, Also, I just noticed from your sessionInfo, the version of the remapped CDF (hgu133plus2hsentrezgcdf_11.0.1) and probe (hgu133plus2hsentrezgprobe_12.0.0) files do not match. One is from the v11 release, the other from v12. I think that is *really* causing the problem your facing. Guido > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Zhijin Wu > Sent: 17 November 2009 05:58 > To: Denise Mauldin > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] GCRMA Error > > Hi Denise > > I'll download the dataset and try to reproduce the error > first and get back to you > > Jean > > Denise Mauldin wrote: > > Greetings all, > > > > I'm running gcrma on arrays from GSE9171 and I'm getting > the infamous > > 'NAs are not allowed in subscripted assignments' error. > > > > > >> GSE9171_GPL570_gcrma <- gcrma(GSE9171_GPL570) > >> > > Adjusting for optical effect..............................Done. > > Computing affinities.Error in tmp.exprs[pmIndex[subIndex]] = apm : > > NAs are not allowed in subscripted assignments > > > >> traceback() > >> > > 3: compute.affinities(cdfName(object), verbose = verbose) > > 2: bg.adjust.gcrma(object, affinity.info = affinity.info, > > affinity.source = affinity.source, > > NCprobe = NCprobe, type = type, k = k, stretch = stretch, > > correction = correction, GSB.adjust = GSB.adjust, rho = rho, > > optical.correct = optical.correct, verbose = verbose, fast = > > fast) > > 1: gcrma(GSE9171_GPL570) > > > >> compute.affinities(cdfname="HGU133Plus2_Hs_ENTREZG", verbose=TRUE) > >> > > Computing affinities.Error in tmp.exprs[pmIndex[subIndex]] = apm : > > NAs are not allowed in subscripted assignments > > > > Is this an error in the HGU133Plus2_Hs_ENTREZG CDF from brainarray? > > Is there something I can do to fix this? > > > > Thanks, > > Denise > > > > > >> sessionInfo() > >> > > R version 2.9.1 (2009-06-26) > > x86_64-unknown-linux-gnu > > > > locale: > > > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US > > > .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N > > > AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI > > FICATION=C > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] hgu133plus2hsentrezgprobe_12.0.0 AnnotationDbi_1.6.1 > > [3] hgu133plus2hsentrezgcdf_11.0.1 gcrma_2.16.0 > > [5] Biostrings_2.12.10 IRanges_1.2.3 > > [7] limma_2.18.3 affy_1.22.1 > > [9] Biobase_2.4.1 > > > > loaded via a namespace (and not attached): > > [1] affyio_1.12.0 DBI_0.2-4 preprocessCore_1.6.0 > > [4] RSQLite_0.7-3 splines_2.9.1 tools_2.9.1 > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > -- > ------------------------------------------- > Zhijin (Jean) Wu > Assistant Professor of Biostatistics > Brown University, Box G-S121 > Providence, RI 02912 > > Tel: 401 863 1230 > Fax: 401 863 9182 > http://www.stat.brown.edu/zwu > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > >
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Hi Guido, Thank you very much for getting to this before I did. Denise, Please let me know if matching the CDF and probe packages versions solves your problem. Jean Hooiveld, Guido wrote: > Hi again, > > Also, I just noticed from your sessionInfo, the version of the remapped > CDF (hgu133plus2hsentrezgcdf_11.0.1) and probe > (hgu133plus2hsentrezgprobe_12.0.0) files do not match. One is from the > v11 release, the other from v12. I think that is *really* causing the > problem your facing. > > Guido > > > >> -----Original Message----- >> From: bioconductor-bounces at stat.math.ethz.ch >> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Zhijin Wu >> Sent: 17 November 2009 05:58 >> To: Denise Mauldin >> Cc: bioconductor at stat.math.ethz.ch >> Subject: Re: [BioC] GCRMA Error >> >> Hi Denise >> >> I'll download the dataset and try to reproduce the error >> first and get back to you >> >> Jean >> >> Denise Mauldin wrote: >>> Greetings all, >>> >>> I'm running gcrma on arrays from GSE9171 and I'm getting >> the infamous >>> 'NAs are not allowed in subscripted assignments' error. >>> >>> >>>> GSE9171_GPL570_gcrma <- gcrma(GSE9171_GPL570) >>>> >>> Adjusting for optical effect..............................Done. >>> Computing affinities.Error in tmp.exprs[pmIndex[subIndex]] = apm : >>> NAs are not allowed in subscripted assignments >>> >>>> traceback() >>>> >>> 3: compute.affinities(cdfName(object), verbose = verbose) >>> 2: bg.adjust.gcrma(object, affinity.info = affinity.info, >>> affinity.source = affinity.source, >>> NCprobe = NCprobe, type = type, k = k, stretch = stretch, >>> correction = correction, GSB.adjust = GSB.adjust, rho = rho, >>> optical.correct = optical.correct, verbose = verbose, fast = >>> fast) >>> 1: gcrma(GSE9171_GPL570) >>> >>>> compute.affinities(cdfname="HGU133Plus2_Hs_ENTREZG", verbose=TRUE) >>>> >>> Computing affinities.Error in tmp.exprs[pmIndex[subIndex]] = apm : >>> NAs are not allowed in subscripted assignments >>> >>> Is this an error in the HGU133Plus2_Hs_ENTREZG CDF from brainarray? >>> Is there something I can do to fix this? >>> >>> Thanks, >>> Denise >>> >>> >>>> sessionInfo() >>>> >>> R version 2.9.1 (2009-06-26) >>> x86_64-unknown-linux-gnu >>> >>> locale: >>> >> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US >> .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N >> AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI >>> FICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] hgu133plus2hsentrezgprobe_12.0.0 AnnotationDbi_1.6.1 >>> [3] hgu133plus2hsentrezgcdf_11.0.1 gcrma_2.16.0 >>> [5] Biostrings_2.12.10 IRanges_1.2.3 >>> [7] limma_2.18.3 affy_1.22.1 >>> [9] Biobase_2.4.1 >>> >>> loaded via a namespace (and not attached): >>> [1] affyio_1.12.0 DBI_0.2-4 preprocessCore_1.6.0 >>> [4] RSQLite_0.7-3 splines_2.9.1 tools_2.9.1 >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> -- >> ------------------------------------------- >> Zhijin (Jean) Wu >> Assistant Professor of Biostatistics >> Brown University, Box G-S121 >> Providence, RI 02912 >> >> Tel: 401 863 1230 >> Fax: 401 863 9182 >> http://www.stat.brown.edu/zwu >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > -- ------------------------------------ Zhijin (Jean) Wu Assistant Professor of Biostatistics Brown University, Box G-S121 Providence, RI 02912 Tel: 401 863 1230 Fax: 401 863 9182 http://www.stat.brown.edu/zwu
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That does appear to be the problem. Is there an easy way to make sure that something like that doesn't happen again? I don't recall installing any of those packages by hand. Thanks, Denise On Tue, Nov 17, 2009 at 8:18 AM, Zhijin Wu <zwu at="" stat.brown.edu=""> wrote: > > Hi Guido, > ?Thank you very much for getting to this before I did. > > Denise, > ?Please let me know if matching the CDF and probe packages versions solves > your problem. > > Jean > > Hooiveld, Guido wrote: >> >> Hi again, >> >> Also, I just noticed from your sessionInfo, the version of the remapped >> CDF (hgu133plus2hsentrezgcdf_11.0.1) and probe >> (hgu133plus2hsentrezgprobe_12.0.0) files do not match. One is from the >> v11 release, the other from v12. I think that is *really* causing the >> problem your facing. >> >> Guido >> >> >>> >>> -----Original Message----- >>> From: bioconductor-bounces at stat.math.ethz.ch >>> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Zhijin Wu >>> Sent: 17 November 2009 05:58 >>> To: Denise Mauldin >>> Cc: bioconductor at stat.math.ethz.ch >>> Subject: Re: [BioC] GCRMA Error >>> >>> Hi Denise >>> >>> I'll download the dataset and try to reproduce the error first and get >>> back to you >>> >>> Jean >>> >>> Denise Mauldin wrote: >>>> >>>> Greetings all, >>>> >>>> I'm running gcrma on arrays from GSE9171 and I'm getting >>> >>> the infamous >>>> >>>> 'NAs are not allowed in subscripted assignments' error. >>>> >>>> >>>>> >>>>> GSE9171_GPL570_gcrma <- gcrma(GSE9171_GPL570) >>>>> >>>> >>>> Adjusting for optical effect..............................Done. >>>> Computing affinities.Error in tmp.exprs[pmIndex[subIndex]] = apm : >>>> ?NAs are not allowed in subscripted assignments >>>> >>>>> >>>>> traceback() >>>>> >>>> >>>> 3: compute.affinities(cdfName(object), verbose = verbose) >>>> 2: bg.adjust.gcrma(object, affinity.info = affinity.info, >>>> affinity.source = affinity.source, >>>> ? ? ? NCprobe = NCprobe, type = type, k = k, stretch = stretch, >>>> ? ? ? correction = correction, GSB.adjust = GSB.adjust, rho = rho, >>>> ? ? ? optical.correct = optical.correct, verbose = verbose, fast = fast) >>>> 1: gcrma(GSE9171_GPL570) >>>> >>>>> >>>>> compute.affinities(cdfname="HGU133Plus2_Hs_ENTREZG", verbose=TRUE) >>>>> >>>> >>>> Computing affinities.Error in tmp.exprs[pmIndex[subIndex]] = apm : >>>> ?NAs are not allowed in subscripted assignments >>>> >>>> Is this an error in the HGU133Plus2_Hs_ENTREZG CDF from brainarray? >>>> Is there something I can do to fix this? >>>> >>>> Thanks, >>>> Denise >>>> >>>> >>>>> >>>>> sessionInfo() >>>>> >>>> >>>> R version 2.9.1 (2009-06-26) >>>> x86_64-unknown-linux-gnu >>>> >>>> locale: >>>> >>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US >>> .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N >>> AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI >>>> >>>> FICATION=C >>>> >>>> attached base packages: >>>> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >>>> >>>> other attached packages: >>>> [1] hgu133plus2hsentrezgprobe_12.0.0 AnnotationDbi_1.6.1 >>>> [3] hgu133plus2hsentrezgcdf_11.0.1 ? gcrma_2.16.0 >>>> [5] Biostrings_2.12.10 ? ? ? ? ? ? ? IRanges_1.2.3 >>>> [7] limma_2.18.3 ? ? ? ? ? ? ? ? ? ? affy_1.22.1 >>>> [9] Biobase_2.4.1 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] affyio_1.12.0 ? ? ? ?DBI_0.2-4 ? ? ? ? ? ?preprocessCore_1.6.0 >>>> [4] RSQLite_0.7-3 ? ? ? ?splines_2.9.1 ? ? ? ?tools_2.9.1 >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>> >>> -- >>> ------------------------------------------- >>> Zhijin (Jean) Wu >>> Assistant Professor of Biostatistics >>> Brown University, Box G-S121 >>> Providence, RI ?02912 >>> >>> Tel: 401 863 1230 >>> Fax: 401 863 9182 >>> http://www.stat.brown.edu/zwu >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >> > > > -- > ------------------------------------ > Zhijin (Jean) Wu > Assistant Professor of Biostatistics > Brown University, Box G-S121 > Providence, RI ?02912 > > Tel: 401 863 1230 > Fax: 401 863 9182 > http://www.stat.brown.edu/zwu > >
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