Question

Trying to annotate microarray data and some probe set presents mismatch

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arronar • 0

@arronar-12722

Last seen 6.9 years ago

Hello.

I'm trying three days now to figure out how to fix this issue with an automatic way but so far couldn't fix it.

Here is the story.

I'm trying to analyse a dataset that has been produced on Affymetrix GeneChip Human Genome U133 Plus 2.0 . After applying RMA algorithm , I used the following code to create annotation columns with GENE SYMBOL and ENTREZ ID within my expression data.frame.

probes=row.names(expressions)
Symbols = unlist(mget(probes, hgu133plus2SYMBOL, ifnotfound=NA))
Entrez_IDs = unlist(mget(probes, hgu133plus2ENTREZID, ifnotfound=NA))
expressions=cbind(probes,Symbols,Entrez_IDs,expressions)

After that I figured out that some probe ids (total 11734) have not any GENE SYMBOL / ENTREZ ID and that is caused, maybe due to the update of the annotation database. I search on net to find out an automatic solution and until now I found this site where I chose to convert Affy IDs --> Gene symbol. Then I supply to it a list of some unidentified probe ids and hit submit

1007_s_at
1294_at
1552283_s_at
1552388_at
1552401_a_at
1552411_at
1552412_a_at
1552449_a_at
1552563_a_at
1552607_at

The thing now is that for some of them, this tool , return two gene symbols and I don't know which to choose.

What do you guys do in such cases ?

Thank you.

annotation affymetrix microarrays • 1.4k views

ADD COMMENT • link updated 7.0 years ago by James W. MacDonald 67k • written 7.0 years ago by arronar • 0

score 1 · Answer 1 · 2017-11-22

The way you originally annotated returns nothing for any one to many mappings. Which is one thing you can do ( e.g., it's not clear what the probeset measures, so return nothing). Another alternative is to select one of the choices, at random, or maybe just the first. The remaining alternative is to return all choices and sort that out when you look at your top hits. Each alternative has its positive and negative aspects, and as the analyst you have to decide which one is right for you.