Hello,
I have been trying to run the ComBat function for a while on my gene array
data but don't manage to make it work. I always get the following error:
Error in solve.default(t(des) %*% des) : Lapack routine dgesv: system is
exactly singular: U[34,34]=0.

I know it is an error of matrice but I do not know how to solve it.

Here are the lines I wrote:

library(“sva”)

mydata = read.table("normalized_data_ filtered_low.txt")

sampleinfo=read.table("sampleinfo.txt”, header=TRUE)

batch = sampleinfo$Batch

mod <- model.matrix(~as.factor(sampleinfo$Phenotype) +
~as.factor(sampleinfo$Status) + ~as.factor(sampleinfo$RF) +
~as.factor(sampleinfo$Responder) + sampleinfo$Age + sampleinfo$DAS +
sampleinfo$TJC28 + sampleinfo$SJC28)
ComBat(dat, batch, mod, numCovs=NULL, par.prior=TRUE, prior.plots=FALSE)


after running it finds 8 covariates and 33 batches and I have 202 samples.


The tab files are as follows:

         sampleinfo file:


gene expression file:



Could you please tell me what could be done to solve this issue.

Giulia

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