[BioC] problems using simpleaffy

Crispin Miller CMiller at PICR.man.ac.uk
Wed Mar 23 13:53:02 CET 2005

Hi Georg,
The scale factors do indeed look somewhat odd - can you tell me what array type you're looking at, and what OS you're running on?


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Georg Otto
Sent: 22 March 2005 21:43
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] problems using simpleaffy

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...
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



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