[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.


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
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>Search the archives: 

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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