[BioC] Affymetrix analysis

fhong@salk.edu fhong at salk.edu
Thu Jul 7 19:30:39 CEST 2005

> Hello,
> I have a couple of questions regarding Affymetrix analysis. We have 4
>> independent experiments analysing control vs test. The experiments are
>> analysing different cell types with a common phenotype with the aim of
>> identifying genes associated with this phenotype. The first question is
>> - is it okay to cross compare the individual experiments with each other
>> even though
>> they were performed independently?
Independence is good. But if you use different type of cells, I don't
think you can cross compare them. One possible analysis is to compare test
vs control for each cell type and combine them into one analysis to
identify genes that are associated with this particular phenotype, you can
check out RankProd package.

>> Secondly, one of the control vs test
>> experiments has been performed on the Mouse Genome 430 2.0 array, whilst
>> the
>> remaining  experiments were performed on the updated version 430A 2.0.
>> So far,
>> with the individual experiments we have been performing analysis using
>> GCRMA on
>> R, but due to the differing probe sets we can’t perform GCRMA whilst
>> including
>> the samples from the old chip version. Is there any possible way that
>> this can
>> be achieved?
If your goal is to identify differentially expressed genes, you can use
RankProd package which can combine data from different platforms into one

Hope this helps


> Thanks in advance
> Christy
> --
> Christy Toms D.Phil
> Sir William Dunn School of Pathology
> Oxford OX1 3RE
> 01865 285489
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Fangxin Hong  Ph.D.
Plant Biology Laboratory
The Salk Institute
10010 N. Torrey Pines Rd.
La Jolla, CA 92037
E-mail: fhong at salk.edu
(Phone): 858-453-4100 ext 1105

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