Its possible that there is a real difference, see this paper for something
similar:

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0011657

Hard to say though without knowing more about the biological question and
just how significant the p-values are.

Paul

On Mon, Mar 19, 2012 at 3:36 AM, Alexandra Muñoz <abm362@nyu.edu> wrote:

> Hi Jim et. al,
>
> I am attempting to analyze data from humans exposed to arsenic in vivo from
> an affymetrix Human Gene 1.0 ST Array. I have generated differentially
> expressed genes lists using LIMMA and an ANOVA.
>
> I am encountering a high number of control probes as top genes in both
> lists and am not sure if I should be ignoring this information, removing
> it, or utilizing it. I found an earlier post which seemed to be related and
> which directed the user to identify the type of probe in order to determine
> if its differential expression may have been an error resulting from batch
> effects (
>
> http://article.gmane.org/gmane.science.biology.informatics.conductor/28952/match=control+probes
> )
> though based on the category of my probes I'm not sure how to proceed.
> NetAffx online tool my control probes fall into the category of  "intronic
> normalization control".     It doesn't make sense to me that they would be
> in the top genes list, and I would appreciate any help as to how to
> interpret their presence and if necessary about how to remove them from the
> analysis prior to the list generation.
>
> Here is an example of some the probe numbers I am getting
>  7892503  7892505  7892551  7892558  7892571  7892581  7892589  7892633
> 7892675  7892676  7892689  7892729  7892738  7892753  7892757  7892788
>
> Thank you,
> Alexandra Munoz
> NYU PhD Student - Molecular and genetic toxicology
>
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>
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>



-- 
Paul Geeleher (PhD Student)
School of Mathematics, Statistics and Applied Mathematics
National University of Ireland
Galway
Ireland
--
www.bioinformaticstutorials.com

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