[BioC] microarray: dealing with multi probes for one gene
Naomi Altman
naomi at stat.psu.edu
Mon May 21 14:50:26 CEST 2007
We found that on our arrays, if we avoided e.g. domains common to
many genes in a family, probes from the same gene had the same
expression pattern on the logarithmic scale, although different
average detection. (Try graphing the probes by condition and see if
the profiles are parallel.)
Given that satisfactory result, for each gene we picked the probe
that was about 2nd highest on most conditions. This was arbitrary -
we felt that probes that had higher level of detections were likely
to avoid being below detection in tissues where they actually
expressed, and I worried that the highest probe might include some
extreme values that were just errors.
--Naomi
At 04:19 AM 5/21/2007, Christophe Boutte wrote:
>Dear Bioconductors users,
>
>I make a post doc in the oceanic research station of Roscoff (France).
>
>I use the limma bioconductor for analysing microarray results.
>There is on my microarrays three replicates for each spot (thus I use
>correlation or average to deal with these values).
>My problem is that we have several probes for each gene on the
>microarray: we designed 1 to 5 different probes for each gene, and I do
>not know how to use them:
>Should I average them ? It's difficult because the number of probes vary
>depending of each gene (1-5) and I cannot precise the number of "dups".
>I can also use correlation, but I have the same problem of variable
>number of probes.
>Has somebody already dealt with this type of problem of variable
>multi-probes by gene ?
>
>thank you in advance,
>
>Christophe Boutte
>
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Naomi S. Altman 814-865-3791 (voice)
Associate Professor
Dept. of Statistics 814-863-7114 (fax)
Penn State University 814-865-1348 (Statistics)
University Park, PA 16802-2111
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