[BioC] RMA normalization issue

[Fuying Gao]

Dear List,

I got error as follows when normolizing a AffyBatch Object (400  
samples) with R 2.9.0.  It works on an old version of R, R 2.6.1, on  
another computer but the computer can not handle so many samples due  
to memory issue.
There is no problem to read in the cel files from both versions of R.


Error in rma(dat) :
   VECTOR_ELT() can only be applied to a 'list', not a 'character'

#dat is the AffyBatch Object

#session info is as follows (got the above error):

> sessionInfo()

R version 2.9.0 (2009-04-17)
x86_64-redhat-linux-gnu

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

other attached packages:
  [1] hgu133acdf_2.2.0     annaffy_1.12.1       KEGG.db_2.2.0
  [4] GO.db_2.2.0          RSQLite_0.6-8        DBI_0.2-4
  [7] AnnotationDbi_1.4.3  gplots_2.6.0         gdata_2.4.2
[10] gtools_2.5.0         MASS_7.2-46          RColorBrewer_1.0-2
[13] affyPLM_1.16.0       simpleaffy_2.16.0    gcrma_2.12.1
[16] matchprobes_1.12.0   genefilter_1.20.0    survival_2.35-4
[19] affy_1.18.1          preprocessCore_1.2.0 affyio_1.8.0
[22] marray_1.18.0        limma_2.14.4         Biobase_2.2.2

loaded via a namespace (and not attached):
[1] annotate_1.18.0





#session info is as follows (no error, an older version R):

> sessionInfo()

R version 2.6.1 (2007-11-26)
i386-pc-mingw32

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

other attached packages:
  [1] hgu133plus2cdf_2.0.0 annaffy_1.10.0       KEGG_2.0.0           GO_2.0.0
  [5] gplots_2.3.2         gdata_2.3.1          gtools_2.4.0          
MASS_7.2-38
  [9] RColorBrewer_1.0-1   affyPLM_1.14.0       simpleaffy_2.14.02    
gcrma_2.10.0
[13] matchprobes_1.10.0   genefilter_1.16.0    survival_2.34         
affy_1.16.0
[17] preprocessCore_1.0.0 affyio_1.6.0         marray_1.16.0         
limma_2.12.0
[21] Biobase_1.16.0


It would be great if someone could help figure out what caused the error.
Thank you!

Fuying Gao