[BioC] Analysis of Affymetrix Mouse Gene 2.0 ST arrays

cstrato cstrato at aon.at
Tue Mar 5 23:13:48 CET 2013

Dear Kamila,

The reason why affy does not work well with WT arrays is that these 
arrays do not have PM/MM pairs in contrast to the ivt arrays for which 
affy was created.

As the author of package xps I can only say that xps does use the 
original library files and annotation files from Affymetrix. The example 
script in directory xps/examples/script4schemes.R will show you how to 
create a scheme file for e.g. MoGene-2_0-ST arrays. However, if you 
decide to use xps I must mention that there is currently a problem with 
the Afymetrix annotation files for the 2.0 and 2.1 arrays, see:
So you need either adapt the mentioned perl script to correct the 
annotation files, or I can send you the modified perl script for 
MoGene-2_0. If you prefer I could also send you the finished 
'mogene20st.root' file, however it has a size of 35 MB so you would need 
to tell me how to send it to you.

BTW, RMA is fine for both ivt arrays and WT arrays. However, if you want 
to get present calls P/M/A then for ivt arrays you need to call 
mas5.call() while for WT arrays you need to call dabg.call().

Best regards,

On 3/5/13 10:45 PM, Naxerova, Kamila wrote:
> Dear all,
> I am analyzing a set of Affymetrix Mouse Gene 2.0 ST arrays. I am quite familiar with 3'-biased chips, but this is my first time looking at data from WT arrays. I have a few general questions -- any advice would be appreciated to speed up my learning process.
> 1) I have already read on this mailing list that the good old affy package does not work well with WT arrays (can anybody point me to any literature on why that is?). So I have installed the oligo and xps packages -- what are the advantages/disadvantages for each? Any opinions on which one is the right "starter kit"?
> 2) I see with some dread that there seems to be no annotation package for the 2.0 array yet. I have never built my own... any quick bullet points on how I would go about doing that for a WT array?
> 3) It seems that RMA is also used for normalization of WT arrays, so that part I am comfortable with. But are there any differences in preprocessing between 3' and WT arrays that I should watch out for?
> Thanks so much!
> Kamila
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