When Analysing Illumina (HT-12) microarrays, I always tend to find that there are NAs returned in some cases (gene name and description) as being differentially expressed. How is something determined to be an NA, I thought they Illumina database would have an entry for every probe sequence used.... Any explanations?
Thanks
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andrew.j.skelton73
Bioconductor -> get nuIDs from probe -> query for gene name and description
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written
by
andrew.j.skelton73
I think you're right. If there's 47K probes on the Illumina HT-12 arrays, There are ~20K protein coding genes in the human genome, 13K Pseudo Genes, I guess that anything that's not associated with a gene is not annotated. I pulled out a few NA entries and their probe sequences, and they all mapped to Pseudogenes on the human genome
Just a sidenote but keep in mind that you are relying on whoever annotates nuIDs to go from probes->genes. Different annotation sources are in different states of outdated-ness. I know some of the genes on HT-12 used to be annotated as pseudo-genes but then were found not to be real so you could sometimes get the case of depreciated Entrez IDs (depending once again on what annotation source you use).
You can blat the probe sequence against the genome in UCSC genome browser and that can help in some cases.
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what software are you using?
Bioconductor -> get nuIDs -> query for gene name and description