Converting Probe IDs to GENE IDs for non-standard microarray

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4.7 years ago

james.wordsworth2 • 0

Hi,

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

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.

microarray probe IDs • 1.8k views

ADD COMMENT • link 4.7 years ago by james.wordsworth2 • 0

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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 REPLY • link 4.7 years ago by JC 13k

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

ADD REPLY • link 4.7 years ago by james.wordsworth2 • 0

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Align them to Ensembl transcripts

ADD REPLY • link 4.7 years ago by JC 13k

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