Question: How to identify lncRNAs from a probe set?
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gravatar for dz2353
11 weeks ago by
dz235380
dz235380 wrote:

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 • 125 views
ADD COMMENTlink written 11 weeks ago by dz235380

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 REPLYlink written 10 weeks ago by Kevin Blighe46k
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