How to identify lncRNAs from a probe set?

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4.9 years ago

dz2353 ▴ 120

Hi, there,

I downloaded a microarray from the GEO database. The platform is GPL6244 [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version]. I used a package from Bioconductor to transform the prob id to Ensembl id. After that, I downloaded the lncRNA annotation from GENCODE, the latest release and found out all of the Ensembl ids of lncRNA. What I want to do is get all of the lncRNA from the probe set. But the result is only 500 or so. A paper used the same microarray and got about 5000 lncRNA. Is there anything wrong with me? Or who can give me some advice about how to get the lncRNA from a probe set. I also want to get the lncRNA from TCGA dataset. Thanks in advance!

Best,

Issac

RNA-Seq • 1.1k views

ADD COMMENT • link 4.9 years ago by dz2353 ▴ 120

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Can you show the processing steps that you used? Note that you can automate the search for the gene biotype, even from the Affy probe IDs. I show an example here: A: Affymetrix Human Genome U133 Plus 2.0 Array

ADD REPLY • link 4.9 years ago by Kevin Blighe 87k

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