Awesome news. Glad you figured it out!


On Jan 16, 2014, at 3:33 PM, Jordan Ramsey wrote:

Hi Evan,

I figured out what was going wrong - my batch variable was a character variable. This worked when all the covariates in the model were factors, but not when some were numerical. I changed the batch variable to a factor and it runs without errors now.

Thanks,
Jordan


On Thu, Jan 16, 2014 at 7:27 PM, Johnson, William Evan <wej@bu.edu<mailto:wej@bu.edu>> wrote:
Hi Jordan,

Sounds like a confounding issue. Are your covariates +  batch linearly independent? In other words are there covariate levels or combinations that are nested within batch?

Evan


On Jan 16, 2014, at 12:54 PM, Jordan Ramsey wrote:

> Hi there,
>
> I've been working with the ComBat function in the SVA package and I've found that there seems to be a problem when trying to include numerical covariates in the model. I consistently get the error:
>
> Error in t(design) %*% design :
>   requires numeric/complex matrix/vector arguments
>
> For example, if I run:
>
> model = model.matrix(~as.factor(Sex) + as.numeric(Age))
> ComBat_dat = ComBat(gene_express, batch = BatchNums, mod = model, numCovs = 3, prior.plots = TRUE)
>
> This produces:
> Found 26 batches
> Found 1  categorical covariate(s)
> Found 1  continuous covariate(s)
> Standardizing Data across genes
> Error in t(design) %*% design :
>   requires numeric/complex matrix/vector arguments
>
> However, when I use a model that only includes factors, I don't get any errors. Any ideas on what is going wrong here? Any help would be appreciated.
>
> Thanks,
> --
> Jordan Ramsey
>




--
Jordan Ramsey
PhD candidate (Biotechnology)
Bahn Group
Department of Chemical Engineering & Biotechnology
University of Cambridge



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