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broadinstitute / ssGSEA2.0

Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
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bug in combine mode #9

Closed yksaito closed 1 year ago

yksaito commented 5 years ago

Hi, I want to run ssGSEA with "combine.add" mode. I modified ssgsea-gui.R to add combine.mode parameter.

## run ssGSEA
    gsea.res <- ssGSEA2(input.ds, ...   , combine.mode= "combine.add")

But this gives an error.

Error in matrix(ol.matrix.2[locs, ], nrow = length(locs)) :
  object 'ol.matrix.2' not found

I don't see any error without combine.mode parameter. I wonder it might be a bug?

karstenkrug commented 5 years ago

Yes, this is a bug. I did not pay much attention to the "combine.mode"-parameter when re-implementing parts of the original ssGSEA code. I will certainly look into this. Thanks, K

hd00ljy commented 3 years ago

Hello,

The same error here.

I found out that the ol.matrix.2 is defined before the problematic line only when the combine mode is off.

In the other cases, ol.matrix.2 is not defined at all

Hope it helps