[BioC] problem to read .CEL file

pingzhao Hu phu at sickkids.ca
Tue Aug 17 01:33:39 CEST 2004


Hi all,
I have a affy dataset ( hgu95av2cdf ) which has 207 arrays.
One of these .CEL files can not be read from our supercomputer.
The error message is as follows:

 > myaffybatch<-ReadAffy(verbose=TRUE)
1 reading /export/scratch4/pinghu/CL2001031608AA.CEL ...done.
instanciating an AffyBatch (intensity a 409600x207 matrix)...done.
2 reading /export/scratch4/pinghu/CL2001031611AA.CEL ...done.
3 reading /export/scratch4/pinghu/CL2001031612AA.CEL ...done.
4 reading /export/scratch4/pinghu/CL2001031613AA.CEL ...done.
5 reading /export/scratch4/pinghu/CL2001031615AA.CEL ...done.
6 reading /export/scratch4/pinghu/CL2001031616AA.CEL ...done.
7 reading /export/scratch4/pinghu/CL2001031618AA.CEL ...done.
8 reading /export/scratch4/pinghu/CL2001031622AA.CEL ...done.
9 reading /export/scratch4/pinghu/CL2001031625AA.CEL ...done.
---------------------------------------------------------------------------------------------
191 reading /export/scratch4/pinghu/CL2001032846AA.CEL ...done.
192 reading /export/scratch4/pinghu/CL2001032848AA.CEL ...done.
193 reading /export/scratch4/pinghu/CL2001032856AA.CEL ...done.
194 reading /export/scratch4/pinghu/CL2001032857AA.CEL ...Error in 
read.celfile(filenames[[i]], compress = compress, rm.mask = rm.mask,  :
         Cannot open the file /export/scratch4/pinghu/CL2001032857AA.CEL
------------------------------------------------------------------------------------------------------

actually this file (CL2001032857AA.CEL) I can read it from my pc machine.

The verion of R on supercomputer is 1.7 and the version of R on my pc 
machine is 1.9.

How can I solve this problem????

Thanks

pingzhao



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