[BioC] 217216_x_at is NOT dihydrolipoamide S-succinytransferase

James W. MacDonald jmacdon at med.umich.edu
Wed Mar 30 15:55:11 CEST 2005

Kevin Dawson wrote:
> Dear Robert,
> I understand, you don't have the resorces to hand-curate the data. I did 
> not know how the info is propagated from Affy (who is selecting the 
> probesets) to the BioConductor packages.
> However, you could have picked up this annotation error automatically. 
> AC006530 is a long piece of DNA that includes both DLST and MLH3 among 
> others (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?
> db=gene&cmd=search&term=AC006530). If you used the info from Affymetrix, 
> where the oligos are, it would have become clear that the oligoset is in 
> MLH3 and not in DLST.

You might note that arguing about the annotation of an _x_at probeset is 
probably not worth the trouble. From the Affy website:

Occasionally, it is not possible to select either a unique probe set or 
a probe set with all probes common among multiple transcripts ("_s_at" 
). In such cases, similarity criteria are suspended, and the resulting 
probe set name is appended with the "_x_at" extension. These probe sets 
contain some probes that are identical, or highly similar, to unrelated 
sequences. These probes may cross-hybridize in an unpredictable manner 
with sequences other than the main target. Data generated from these 
probe sets should be interpreted with caution, due to the likelihood 
that some of the signal is from transcripts other than the one being 
intentionally measured.

In other words, you probably aren't measuring what you think anyway.



> Thanks anyway,
> Kevin
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James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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