[BioC] Fwd: covariate information
jung.cholhee at gmail.com
Wed Oct 24 04:10:22 CEST 2012
Below is the question I posted originally in the 'ComBat user forum' of
But, as I was suggested to forward my question to Bioconductor mailing
list, I'm doing it now.
Please find my question, below.
On Tuesday, October 23, 2012 10:13:26 AM UTC+11, Cholhee Jung wrote:
> Dear users,
> I was trying ComBat on ~1,000 samples.
> Samples are spread over 12 batches and each batch contains 4 technical
> replicates that are identical across all batches.
> The number of covariates is 5, and I was using the ComBat implemented in
> the 'sva' package.
> I tried ComBat with two model matrix built from the same covariate
> First model matrix was constructed as below:
> >mod_mat = model.matrix(~as.factor(cov1) + as.factor(cov2) +
> as.factor(cov3) + as.factor(cov4) + as.factor(cov5), data=pheno_data )
> Second one was built as below:
> >mod_mat = model.matrix(~as.factor(paste(pheno_data$cov1,
> pheno_data$cov2, pheno_data$cov3, pheno_data$cov4, pheno_data$cov5,
> Basically, covariates were concatenated into one string for the the
> second model matrix.
> ComBat with the first model matrix raised the 'singular' error like below:
> Error in solve.default(t(design) %*% design) :
> Lapack routine dgesv: system is exactly singular
> But, ComBat run without error with the second model matrix.
> Now I wonder if the two different model matrices are same?
More information about the Bioconductor