[BioC] problems using simpleaffy

Crispin Miller CMiller at PICR.man.ac.uk
Wed Mar 23 16:48:17 CET 2005

Dear Georg,
I've just tried some zebrafish chips and given them a go on my version of simpleaffy (2.10) running on a linux machine. As far as I can tell, the data looks sensible - scale factors are ~0.8 and a quick scatter plot of the expression calls also looks OK.

I suspect this is an issue with compiling/running on a Mac - which is something I'm afraid I have no experience of doing... The other issue - with the subscript out of bounds error is due to the GAPDH probeset id being incorrect in the data files with the package... I've fixed that, and I'll post a patched version in the next few days.



-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Georg Otto
Sent: 23 March 2005 13:29
To: Crispin Miller
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] problems using simpleaffy

Dear Crispin,

I use the affymetrix zebrafish array, my OS is Mac OS 10.2.8.



On Wednesday, March 23, 2005, at 01:53 PM, Crispin Miller wrote:

> 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?
> Crispin
> -----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...
> ..........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

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