[BioC] Combat

[Peter Langfelder]

It's hard to know exactly without seeing your data and code, but
chances are that your model matrix or other sample information does
not contain the same number of samples (rows) as the expression data
(if I recall correctly, ComBat expects samples in columns of the
expression data, so the number of rows of the model matrix must equal
the number of columns of the expression data and the length of the
batch variable).

HTH,

Peter

On Mon, Nov 4, 2013 at 10:28 AM, Kovyrshina, Tatiana
<tkovyrshina at houstonmethodist.org> wrote:
> 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.
>
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