[BioC] Combat

[Kovyrshina, Tatiana]

Hello!

I am trying to run combat on 4 data sets that I got from GEO and I get the following error:

Reading Sample Information File
Reading Expression Data File
Found 4 batches
Found 1 covariate(s)
Found 337 Missing Data Values
Standardizing Data across genes
Error in solve.default(t(des) %*% des) : 
  Lapack routine dgesv: system is exactly singular: U[3,3] = 0

I noticed it had "missing data values" and isolated the problem to the last 200 genes (12,100 good ones left), however I still get the following error when I run the data without the last genes:

Reading Sample Information File
Reading Expression Data File
Found 4 batches
Found 1 covariate(s)
Standardizing Data across genes
Error in ((dat - t(design %*% B.hat))^2) %*% rep(1/n.array, n.array) : 
  non-conformable arguments

Do you have any suggestions what the problem might be? I would very much appreciate your help.

Thank You!
Tatiana K.

Houston Methodist. Leading Medicine.

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