[BioC] simpleaffy problem

[Crispin Miller]

Hi Ariel,
Sorry for taking a few days to reply. I guess the simple answer is that
I don't know, however, I've not had access to a Mac to test simpleaffy
on:

http://bioinformatics.picr.man.ac.uk/simpleaffy/index.jsp

my instinct is that this is where the problem lies - the scale factors
look very odd, and there's a fair amount of C-code interfacing with R
under the bonnet. I'll try to look into things and let you know what I
find. In the meantime try:

 x.mas<-call.exprs(x,"mas5-R"), which uses the R implementation in
expresso instead...

As I said, I've not done any testing on macs so be careful! :-)
Good luck,

Crispin




-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Ariel
Chernomoretz
Sent: 18 August 2004 20:20
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] simpleaffy problem

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.
Centre de recherche du CHUL
2705 Blv Laurier, bloc T-367
Sainte-Foy, Qc
G1V 4G2
(418)-525-4444 ext 46339
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