Entering edit mode
Georg Otto
▴
510
@georg-otto-956
Last seen 10.3 years ago
Hi bioconductors,
I have a problem trying to reproduce the user?s guide of simpleaffy
with my own data. I do it like this:
> x<-read.affy("covdesc")
> x.mas5<-call.exprs(x,"mas5")
Background correcting
Retrieving data from AffyBatch...done.
Computing expression calls...
..........done.
scaling to a TGT of 100 ...Scale factor for: 1.CEL
1.27818905696529e-247
Scale factor for: 2.CEL 8.30729457715284e-252
Scale factor for: 3.CEL 1.27818905696529e-247
Scale factor for: 4.CEL 1.27818905696529e-247
Scale factor for: 5.CEL 2.37641150479280e-156
Scale factor for: 6.CEL 2.37641150479280e-156
Scale factor for: 7.CEL 1.27818905696529e-247
Scale factor for: 8.CEL 1.27818905696529e-247
Scale factor for: 9.CEL 2.37641150479280e-156
Scale factor for: 10.CEL 2.37641150479280e-156
> qc.data<-qc(x, x.mas5)
Getting probe level data...
Computing p-values
Doing PMA Calls
Error in FUN(X[[4]], ...) : subscript out of bounds
First of all , the Scale factors look pretty odd. Secondly, I have no
clue, what the error message means. I would appreciate any hint.
I am running simpleaffy 2.10 with R 2.0.1 on powerpc-apple-darwin6.8
Best,
Georg