[BioC] Is it possible to use RMA on Agilent Data

Ulrike Goebel ugoebel at mpiz-koeln.mpg.de
Tue Mar 11 12:47:22 CET 2008

Hi all,

actually, I have (a) similar question(s)  regarding  a very non-standard 
Agilent data set: this is a custom 60mer oligo chip, the probes of which are 
designed from Arabidopsis thaliana sequence information, but intended to 
measure expression in the related non-model organism Arabis alpina. There are 
several probes per A. thaliana gene (not always the same number per gene). In 
addition, only the green channel has been used, so this is in effect a 
one-channel chip. Altogether, this is *very* similar to an Affymetrix 
experiment, so: is there a (simple ?) way to use the affy methods on it ?


>Hi Srini,
>Not as a whole, but parts of it can apply.
>We actually use the RMA background correction method on our Agilent chips.
>The median polish section for probeset summary would not be applicable. 
>There are no probesets in Agilent Chips, as each probe stands on its own.
>Srinivas Iyyer wrote:
>> Dear group, 
>> This might be a stupid question. can I use RMA on
>> Agilent data. 
>> srini

  Dr. Ulrike Goebel
  Bioinformatics Support
  Max-Planck Institute for Plant Breeding Research
  Carl-von-Linne Weg 10
  50829 Cologne
  +49(0) 221 5062 121

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