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"old" microarray probe IDs conversion to genes

Hello everyone,

I am a total beginner in microarray analysis. I have to analyze an unpublished, old data set. The experiment was performed using Unigeneset RZPD3 microarray chip. My problem is that in my data all the probe ids are like IMAGpXXXNXXXXX, where X is a number and N a letter. I am trying to find an R annotation package to help me transform these ids to gene ids, but i cant find anything helpful. Can anyone help me in any way?

Thanks a lot.

r microarray annotation old_data
• 181 views • link
written by irene768 • irene768

1 answer

It is called Unigeneset RZPD3 and I think this is the resource you need. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3050

Check the table at the bottom.

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written by ATpoint ATpoint

Yes it's Unigene, you are right! I also checked the link and found the annotation table but and these data contain only 37530 ids. My data set has 51145 ids and i need to annotate all of them.

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written by irene768 • irene768

Well, if this on GEO is the official annotation you have to find out why there are more probes in your table. Any more details you can give?

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written by ATpoint ATpoint

i guess that not all of the ids in my data correspond to genes, so i think i solved my problem. thank you for your help!!

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written by irene768 • irene768

Yes, but also not all of the annotation rows in that GPL3050 correspond to genes either, so better be sure before you continue. There are typically plenty of control probes but these must be annotated in the reference as well.

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written by ATpoint ATpoint

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