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Question: Can't make sva comparison despite very distinct batch effects
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I continuously receive this error when I try to run sva with my count data

R code for sva:

# Loading all variables 
dat  <- dds_matrix
idx  <- rowMeans(dat) > 1
dat  <- dat[idx,]
mod  <- model.matrix(~batch, colData(dds))
mod0 <- model.matrix(~1, colData(dds))
svseq <- svaseq(dat, mod, mod0)

I receive this error message.

Error in solve.default(t(mod) %*% mod) : Lapack routine dgesv: system is exactly singular: U[4,4] = 0

I have very distinct batches which can be seen in this plot.

PCA plot of my data set, the colors indicate my batches

I have clearly dictated the batches as factors and this exact process has worked before. This is with a new, but very similar data set.

If it is simply not possible to remove these batch effects, how would I go about bringing these two batches closer together, they are definitely the same condition and the variance is likely due to batch effects, not biological significance.

ADD COMMENTlink 2.0 years ago jjrin • 10
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what is your contrast of interest? if you model sva on your known batch, it will look for covariates that are independet of it.

ADD REPLYlink 2.0 years ago
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