[BioC] simpleaffy problem

[Ariel Chernomoretz]

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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