[R] read.affy.mixed - subscript out of bounds error

Zuzanna zuzanna.makowska at unibas.ch
Tue Dec 8 09:08:49 CET 2009


Hello,
I have a problem with read.affy.mixed function. I want to read in  
together a set of CEL files from chip types Affymettrix HGU133A_2 and  
HGU133_Plus_2. I have my files to be read in in one directory together  
with a white space delimited file describing them (covdesc). In this  
directory I give a command:

 > merge <- read.affy.mixed()
Error in merged[[i]] : subscript out of bounds
Error in cdfName(merged[[i]]) :
   error in evaluating the argument 'object' in selecting a method for  
function 'cdfName'
 > sessionInfo()
R version 2.10.0 (2009-10-26)
x86_64-apple-darwin9.8.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
  [1] hgu133a2.db_2.3.5      hgu133plus2probe_2.5.0  
hgu133plus2.db_2.3.5   org.Hs.eg.db_2.3.6
  [5] RSQLite_0.7-3          DBI_0.2-4               
hgu133a2probe_2.5.0    AnnotationDbi_1.8.1
  [9] hgu133a2cdf_2.5.0      hgu133plus2cdf_2.5.0    
simpleaffy_2.22.0      gcrma_2.18.0
[13] genefilter_1.28.2      affy_1.24.2            Biobase_2.6.0

loaded via a namespace (and not attached):
[1] affyio_1.14.0        annotate_1.24.0      Biostrings_2.14.8     
IRanges_1.4.9
[5] preprocessCore_1.8.0 splines_2.10.0       survival_2.35-7       
tools_2.10.0
[9] xtable_1.5-6

Thanks for your help!
Zuza




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