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









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