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Discrepancy in shown elements for same array using


i typed in the probeset ids and afterwards the correspondig agi ids for the same microarray and experienced that there occured a discrepancy in the shown elements (in pathway "overview"): the total
number for using AGi exceeded the number for using probeset ids, although in some sub-bins the number of shown elements (by using Probeset ids)
were higher.I looked out for several "missing" genes and checked for their existence in my used data containing the probeset ids.These ids did not miss and there is no fault in the data.
the numbers should be equal or not?


Re: Discrepancy in shown elements for same array u
1/31/06 8:29 AM as a reply to Dear Trypton.

I am not sure if I understood your question correctly.

However, if you allude to the fact, that if you translate affy_ids in your experiment file to agi ids and then redisplay that in MM, the total number of genes in bins is different.
That could very well be due to the following facts
i) one can't always assign one and only one AGI Code (Gene number At1g12340) to an Affy Probeset id 264576_x_at
ii) we used our own assignment of TIGR5 AGI codes to Affy Probesets which we only based on the actual probesets present on the chip. TAIR now uses the same strategy for the TAIR6 release see News of January 10th. So with the forthcoming TAIR6 release we will resync with TAIR
iii) Probsets which matched genes with very different functions were moved to BIN 35.3 since here we can't be sure what they are really measuring

I hope this answers your question