Unknown gene names in Clariom D human Gene chip annotation files?
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
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
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See if this helps: https://support.bioconductor.org/p/104885/
shasmar: https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=human&c=Gene&l=shasmar
Thanks Genomax. Can one use such gene names in differentially expressed gene analysis?
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.
Thanks Genomax. Much appreciated.