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Ariel Chernomoretz
▴
380
@ariel-chernomoretz-885
Last seen 10.3 years ago
Hi,
I am trying to reproduce the simpleaffy vignette examples and found
some weird behavior:
I read the cel files
> setwd("GQ002/tissu_06/CEL")
> x<-read.affy("covdesc")
> pData(x)
sample treatment
GQ002F01D06C4R1.CEL 1 n
GQ002F01D06C4R2.CEL 2 n
GQ002F01D06C4R3.CEL 3 n
GQ002F02D06C4R1.CEL 4 g
GQ002F02D06C4R2.CEL 5 g
GQ002F02D06C4R3.CEL 6 g
I get the following when apply mas5 processing method
> x.mas<-call.exprs(x,"mas5")
Background correcting
Retrieving data from AffyBatch...done.
Computing expression calls...
......done.
scaling to a TGT of 100 ...Scale factor for: ./GQ002F01D06C4R1.CEL
8.97428766057367e-15
Scale factor for: ./GQ002F01D06C4R2.CEL 8.97428766057367e-15
Scale factor for: ./GQ002F01D06C4R3.CEL 8.97428766057367e-15
Scale factor for: ./GQ002F02D06C4R1.CEL 8.97428766057367e-15
Scale factor for: ./GQ002F02D06C4R2.CEL 8.97428766057367e-15
Scale factor for: ./GQ002F02D06C4R3.CEL 8.97428766057367e-15
and the following error message while trying to perform a pairwise
comparation:
> results<-pairwise.comparison(x.mas,"treatment",spots=x)
Getting probe level data...
Computing p-values
Doing PMA Calls
Error in get.fold.change.and.t.test(x, group, members, logged =
logged,
:
NA/NaN/Inf in foreign function call (arg 1)
Moreover if I read again the same CEL files and repeat the mas5.0
calculation I get the following new scale factors:
> xx<-read.affy("covdesc")
> xx.mas<-call.exprs(xx,"mas5")
Background correcting
Retrieving data from AffyBatch...done.
Computing expression calls...
......done.
scaling to a TGT of 100 ...Scale factor for: ./GQ002F01D06C4R1.CEL
6.52404421935092e-34
Scale factor for: ./GQ002F01D06C4R2.CEL 29644.0460038727
Scale factor for: ./GQ002F01D06C4R3.CEL 8.45337767106362e-171
Scale factor for: ./GQ002F02D06C4R1.CEL 28417.5423558275
Scale factor for: ./GQ002F02D06C4R2.CEL 8.45337767106362e-171
Scale factor for: ./GQ002F02D06C4R3.CEL 8.45337767106362e-171
Is there a problem reading the cel files? R is not started in the CEL
files directory, is that a problem?
I am running R 1.9.0 on Mac OS X 10.3.5
affy 1.4.30
simpleaffy 1.2.1
Any help would be apreciated
Ariel./
Ariel Chernomoretz, Ph.D.
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