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
[[alternative HTML version deleted]]
______________________________________________
[email protected] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
