[BioC] Affymetrix control genes plus links

[Patrícia Luiza Nunes da Costa]

Thanks for your answers Michal and Jeanette,

I did the analysis with Affy Expression Console. They are at
http://www.divshare.com/download/4115598-f93
The Pearson’s correlation showed 2 or 3 arrays that could be outliers, but
I don’t know what is the limit to consider if they are outliers or not
(the values are very near), do you know?
I observed that many probesets follow the controls' pattern, the
fluorescence intensity are lower in all array (Log probe cel intensity:
http://www.divshare.com/download/4115603-454). The images of the chips are
good; I think there isn’t any damage. We performed the same processing,
scanning etc
Where about what Jeanette said, the internal controls didn’t seem very
different, especially GAPDH
(http://www.divshare.com/download/4115599-597), maybe she have reason and
I shouldn’t worry about it.

What do you think people?

All the best,

Patricia





> Patricia,
>
> The control probe sets are spiked in. It could just be a pipetting error
> during labeling / hybridization. Notice that the beta-Actin probe sets are
> OK. Don't worry about it. Check the Gapdh probe sets (these may vary under
> certain conditions, but usually don't).
>
> Jeanette McClintick, PhD
> Indiana University School of Medicine
> Center for Medical Genomics
> Indianapolis, IN
> 317-274-8488
> jnmcclin at iupui.edu
>
> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Patrícia
> Luiza
> Nunes da Costa
> Sent: Wednesday, March 26, 2008 9:24 AM
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] Affymetrix control genes plus links
>
> Dear colleagues,
>
> We are trying to analyze a group of Affymetrix arrays, but we don’t have
> experience. We performed the RMA normalization and after we analyzed with
> the algorithm SOM (3x3 Expander), among others.
> We observed that some control genes was differentially expressed in 2/12
> arrays (cluster in: http://www.divshare.com/download/4105386-853),
> and it shoudn't, isn't it?
> The QC stats plot (simpleaffy) seemed good
> (http://www.divshare.com/download/4105385-181),
> and all parameters indicated by Affymetrix showed results acceptable.
>
> Do you think we have a bug in the experiment?
>
> Should we compare this 2 “different” arrays with the others? Or can we
> correct this?
>
> Thanks for your help!
>
> Patricia
>
>
>
> Patrícia Luiza Nunes da Costa
> Laboratório de Oncologia Experimental, Grupo de Adesão Celular
> Faculdade de Medicina da Universidade de Paulo-FM USP
> Av. Dr. Arnaldo, 455 sala 4112
> Cerqueira Cesar
> Cep 01246-903
> Tel: (11) 3061-7486 e (11) 8202-7073
>
>
>
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Patrícia Luiza Nunes da Costa
Laboratório de Oncologia Experimental, Grupo de Adesão Celular
Faculdade de Medicina da Universidade de Paulo-FM USP
Av. Dr. Arnaldo, 455 sala 4112
Cerqueira Cesar
Cep 01246-903
Tel: (11) 3061-7486 e (11) 8202-7073



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Esta mensagem foi verificada
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acredita-se estar livre de Virus.