Question: Converting Probe IDs to GENE IDs for non-standard microarray
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gravatar for james.wordsworth2
8 days ago by
james.wordsworth20 wrote:

Hi,

I am trying to get the gene IDs for probes from GSE116761, which uses AGILENT Arraystar Human LncRNA microarray V2.0:

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE116761

However, the probe names are very strange and aren't recognised by ensembl biomart. Most look like this:

ASHG19A3A019218

Any suggestions would be greatly appreciated.

ids microarray probe • 70 views
ADD COMMENTlink modified 8 days ago • written 8 days ago by james.wordsworth20
1

that is a custom array from Agilent, check if they are providing the annotation, but probe sequences are reported in https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL13825

ADD REPLYlink written 8 days ago by JC8.2k

Hi, thanks. Yes I saw the probe sequences. Do you know what package I should use to identify the genes from these?

ADD REPLYlink written 7 days ago by james.wordsworth20

Align them to Ensembl transcripts

ADD REPLYlink written 7 days ago by JC8.2k
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