Dear all,

First, I apologize for the mass email. I've been reading manuals, googling,
searching the archive of the mailing list, but still cannot find an exact
answer to my problem.

(1) Question: Can a large number of CEL files cause an overflow for the
function ReadAffy() in the affy packages? Is there any way to fix this?
Other options seem to be other software RMAExpress and dChip in WindowsXP.
Any suggestions?

(2) Background: What I am trying to do is to read in all the CEL files in
the directory to create an AffyBatch object, so that I can use functions in
the affy package. To be more specific, I want to do RMA, dChip normalization
and get MAplots. In my workstation (48 64-bit CPUs, 500Gb memory),
ReadAffy() worked fine for 241 CEL files, but when I moved on to 2,035 CEL
files, it failed and kept showing the error message below. The number of
rows for the CEL file is roughly 50k. On the bright side, I tried justRMA()
and got the expression values in the text format.

> R
> library(affy)
> Data <- ReadAffy()
Error in read.affybatch(filenames = l$filenames, phenoData
= l$phenoData,  :
  allocMatrix: too many elements specified


FYI, below is the session information on my workstation.

> sessionInfo()
R version 2.7.1 (2008-06-23)
ia64-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_IDENTIFICATION=C

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

other attached packages:
 [1] geneplotter_1.18.0          annotate_1.18.0
 [3] xtable_1.5-2                AnnotationDbi_1.2.2
 [5] RSQLite_0.6-9               DBI_0.2-4
 [7] lattice_0.17-8              BufferedMatrixMethods_1.4.0
 [9] BufferedMatrix_1.4.0        affy_1.18.2
[11] preprocessCore_1.2.0        affyio_1.8.0
[13] Biobase_2.0.1

loaded via a namespace (and not attached):
[1] grid_2.7.1         KernSmooth_2.22-22 RColorBrewer_1.0-2




Thank you so much for reading this and I would appreciate your reply.

Hailong


-- 
Sincerely,

Hailong Cui

Computational Biosciences PSM Program
Graduate Certificate in Statistics Program
Web Page: http://mathpost.asu.edu/~hcui

Graduate Teaching Associate (Instructor)
Department of Mathematics & Statistics
Arizona State University
Tempe, AZ 85287-1804

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