question about qc function in SimpleAffy package with U95Av2 array

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James Anderson ▴ 820

@james-anderson-1641

Last seen 10.2 years ago

Hi, I am trying to use qc function to get those quality measures for a bunch of U95Av2 cel files. Below is part of my script: raw.data = ReadAffy(filenames = fn) x.mas5 <- call.exprs(raw.data,"mas5",sc = 100) qcmas5 = qc(raw.data,x.mas5) There is some error message below: Error in FUN(c("AFFX-r2-Ec-bioB-3_at", "AFFX-r2-Ec-bioC-3_at", "AFFX-r2-Ec-bioD-3_at", : subscript out of bounds In addition: Warning message: In qc.affy(unnormalised, ...) : CDF Environment name ' hgu133acdf ' does not match cdfname ' hgu95av2cdf ' Using the same piece of code, it works perfectly for some U133A array. I am wondering could anyone tell me how to solve this problem? Thanks a bunch, -James [[alternative HTML version deleted]]

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ADD COMMENT • link updated 14.5 years ago by Vincent J. Carey, Jr. 6.7k • written 14.5 years ago by James Anderson ▴ 820

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Vincent J. Carey, Jr. 6.7k

@vincent-j-carey-jr-4

Last seen 9 weeks ago

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hard to diagnose if you don't read the posting guide and supply result of sessionInfo() after the error is thrown. On Fri, May 21, 2010 at 12:32 PM, James Anderson <janderson_net@yahoo.com>wrote: > Hi, > > I am trying to use qc function to get those quality measures for a bunch of > U95Av2 cel files. Below is part of my script: > > raw.data = ReadAffy(filenames = fn) > x.mas5 <- call.exprs(raw.data,"mas5",sc = 100) > qcmas5 = qc(raw.data,x.mas5) > > There is some error message below: > > Error in FUN(c("AFFX-r2-Ec-bioB-3_at", "AFFX-r2-Ec-bioC-3_at", > "AFFX-r2-Ec-bioD-3_at", : > subscript out of bounds > In addition: Warning message: > In qc.affy(unnormalised, ...) : > CDF Environment name ' hgu133acdf ' does not match cdfname ' hgu95av2cdf > ' > > Using the same piece of code, it works perfectly for some U133A array. I am > wondering could anyone tell me how to solve this problem? > > Thanks a bunch, > > -James > > > > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

ADD COMMENT • link 14.5 years ago Vincent J. Carey, Jr. 6.7k

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Hi Vincent, I'll read more carefully about the posting guide. Below is the information I got by typing sessionInfo(), thanks. -James R version 2.10.1 (2009-12-14) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] hgu95av2cdf_2.5.0 heatmap.plus_1.3 hgu133acdf_2.5.0 simpleaffy_2.22.0 [5] gcrma_2.18.1 genefilter_1.28.2 affy_1.24.2 Biobase_2.6.1 loaded via a namespace (and not attached): [1] affyio_1.14.0 annotate_1.24.1 AnnotationDbi_1.8.1 [4] Biostrings_2.14.12 DBI_0.2-5 IRanges_1.4.14 [7] preprocessCore_1.8.0 RSQLite_0.8-4 splines_2.10.1 [10] survival_2.35-7 tools_2.10.1 xtable_1.5-6 --- On Sat, 5/22/10, Vincent Carey <stvjc@channing.harvard.edu> wrote: From: Vincent Carey <stvjc@channing.harvard.edu> Subject: Re: [BioC] question about qc function in SimpleAffy package with U95Av2 array To: "James Anderson" <janderson_net@yahoo.com> Cc: "bioconductor" <bioconductor@stat.math.ethz.ch> Date: Saturday, May 22, 2010, 3:53 PM hard to diagnose if you don't read the posting guide and supply result of sessionInfo() after the error is thrown. On Fri, May 21, 2010 at 12:32 PM, James Anderson <janderson_net@yahoo.com> wrote: Hi, I am trying to use qc function to get those quality measures for a bunch of U95Av2 cel files. Below is part of my script: raw.data = ReadAffy(filenames = fn) x.mas5 <- call.exprs(raw.data,"mas5",sc = 100) qcmas5 = qc(raw.data,x.mas5) There is some error message below: Error in FUN(c("AFFX-r2-Ec-bioB-3_at", "AFFX-r2-Ec-bioC-3_at", "AFFX-r2-Ec-bioD-3_at", : subscript out of bounds In addition: Warning message: In qc.affy(unnormalised, ...) : CDF Environment name ' hgu133acdf ' does not match cdfname ' hgu95av2cdf ' Using the same piece of code, it works perfectly for some U133A array. I am wondering could anyone tell me how to solve this problem? Thanks a bunch, -James [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]

ADD REPLY • link 14.5 years ago James Anderson ▴ 820

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