error with ELMER package
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mcastrod • 0
@mcastrod-10187
Last seen 2.6 years ago

Dear All,

I was trying to use ELMER package with some different TCGA tumor types in order to study enhancers. I had no problems with the test example (LUSC), but when I use another TCGA cancer type (GBM) with the default pipeline TCGA.pipe I get the following error:

Error in (function (mee, probes, nearGenes, percentage = 0.2, permu.size = 10000,  :  Probes option should be subset of row names of methylation matrix.

This error occurs at the beginning of the "Predict pairs" stage. I was checking the results and I think that the error comes from the differential methylation step, so the result files only contains NA values. Someone had this problem?

I was checking also the samples used and I saw that for GBM, the pipeline found 64 tumor samples and 1 control with methylation and expression information, maybe this could be the problem?

Thank you very much.

software error ELMER • 551 views
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lijingya • 0
@lijingya-7830
Last seen 5.9 years ago
United States
The problem comes from 1 control. In the differential methylation steps, more than 1 controls are required. My recommendation is that you can use other source of GBM normal controls. In paper method section (Inferring regulatory element landscapes and transcription factor networks from cancer methylomes), you can find source of extra normal GBM. Thanks.
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