Hello,
I am using Combat over a RNA-seq dataset, transformed with Voom. Combat is giving me a strange error, since my design matrix seems unambiguous.
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#Conditions
> myGroups
[1] b b b b b lgnmi lgnmi lgnmi lgnmi hgnmi hgnmi hgnmi Levels: b hgnmi lgnmi
> d <- calcNormFactors(d)
> v <- voom(d,myDesign,plot=TRUE)
> myDesign myGroupsb myGroupshgnmi myGroupslgnmi myBatch 1 1 0 0 1 2 1 0 0 1 3 1 0 0 1 4 1 0 0 2 5 1 0 0 2 6 0 0 1 1 7 0 0 1 2 8 0 0 1 2 9 0 0 1 2 10 0 1 0 1 11 0 1 0 1 12 0 1 0 2 attr(,"assign") [1] 1 1 1 2 attr(,"contrasts") attr(,"contrasts")$myGroups [1] "contr.treatment"
> ComBat(
dat=as.matrix(v$E),
batch=myBatch,
mod=myDesign[,1:3],
prior.plots=T
)
Found 2 batches Found 3 categorical covariate(s) Standardizing Data across genes Error in solve.default(t(design) %*% design) : system is computationally singular: reciprocal condition number = 1.4803e-17
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Some idea? Thanks
"Some of any two" shoudl have read "Sum of any two"... sorry.
Your own posts have an "edit" link below them that you can use to modify them to fix this error ;-)