[BioC] Inconsistent annotation of affy probeset on Affymetrix chip for rat: 230.2

Christoph Preuss ch.preuss at googlemail.com
Wed Jul 2 17:27:31 CEST 2008

Hi everyone,

We analyzed a global exression microarray data set using gcrma for the
normalization step and limma for finding differentially expressed
genes. One of the most significant probesets (ProbeSetID annotation
"1375535_at") in terms of d.e is annotated as  :
Probeset "1375535_at"
-Gene Symbol: Lpin1
- Location: Chr 6

in the bioconductor package  "rat2302" / "rat2302.db".

We also looked at the Affymetrix web site, where the same probeset was
annoted as "Transcribed sequence" on chromosome X.

Affymetrix Annotation RG 230 2.0 Chip:
-ProbeSetID:	1375535_at
-Target Sequence:	

Interestingly, the given target sequence for the probeset matches only
a mouse sequence and not even a rat mRNA (blastn search).

The question is which annotation should we trust?
Is there any chance to validate the probeset annotation?
Many thanks in advance for any help.


Christoph Preuss

(Leibniz-Institute for Arteriosclerosis Research, University of
Muenster Germany )

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