Question: Unknown gene names in Clariom D human Gene chip annotation files?
1
gravatar for mgab
6 months ago by
mgab50
Germany
mgab50 wrote:

Dear All, I am using Clariom D gene chip (Human). I have performed Differential gene expression (DEG) using the Clariom D Human microarray and used the annotation file (transcript) from the link below

https://www.thermofisher.com/sa/en/home/life-science/microarray-analysis/microarray-data-analysis/genechip-array-annotation-files.html

In the list of DEG, there are many gene names (coding) in lower case letters that I am unable to identify, such as shasmar, tusweyb, nugo etc. Should I use them in analysis? Is there a file which has both probeset ID and its corresponding entrez gene ID (Gene symbol). Thank you

clariom d • 265 views
ADD COMMENTlink modified 6 months ago • written 6 months ago by mgab50

Thanks Genomax. Can one use such gene names in differentially expressed gene analysis?

ADD REPLYlink written 6 months ago by mgab50

If the gene no longer exists in current genome build then I would be hesitant to use them. You could leave them in (if they don't overlap with known current genes) but then not use them for actual downstream analysis.

ADD REPLYlink written 6 months ago by genomax71k

Thanks Genomax. Much appreciated.

ADD REPLYlink written 6 months ago by mgab50
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