Hello,
I am trying to use the SVA package to obtain values after batch effect removal in RNA seq data (using DESeq rld counts),

My design:

design

mod = model.matrix(~strain, data=design)

> mod
                (Intercept) strainWT
Late_mut_count            1        0
mid_mut_count             1        0
mid_WT_count              1        1
Young_mut_count           1        0
Young_WT_count            1        1
mid2_mut_count            1        0
mid2_WT_count             1        1
y2_mut_count              1        0
y2_WT_count               1        1
attr(,"assign")
[1] 0 1
attr(,"contrasts")
attr(,"contrasts")$strain
[1] "contr.treatment"

I am using the DESeq's rld transformation: For the first columns, it looks like this:

gene1       2.719515      2.722055     2.742202        2.673428       2.678986

batch = design$batch



Now, I am trying to use ComBat:

combat_edata = ComBat(dat=rldCounts, batch=batch, mod=mod, numCovs=NULL, par.prior=TRUE)

But I get the following error:

Error in ComBat(dat = rldCounts, batch = batch, mod = mod, numCovs = NULL,  : 
  unused argument (numCovs = NULL)

Can you possibly help with this error please?

Thanks

Don't forget to include the output of sessionInfo() so we know what version you're working with, but anyway: the error is telling you exactly what the problem is.

When I do ?ComBat using the latest version of sva, the help page will show you that the ComBat function only takes five arguments:

• dat
• batch
• mod
• par.prior
• prior.plots

None of which is numCovs.

Thanks a lot!!!

Now I get a different error:

combat_edata = ComBat(dat=rldCounts, batch=batch, mod=mod, par.prior=TRUE)
Found 2 batches
Adjusting for 2 covariate(s) or covariate level(s)
Standardizing Data across genes
Fitting L/S model and finding priors
Finding parametric adjustments
Error in while (change > conv) { : missing value where TRUE/FALSE needed

Can you help with this please?

===========================================

Here is the sessionInfo:

sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 8 x64 (build 9200)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] DESeq2_1.8.1              RcppArmadillo_0.5.200.1.0 Rcpp_0.11.6               GenomicRanges_1.20.5     
 [5] GenomeInfoDb_1.4.1        IRanges_2.2.5             S4Vectors_0.6.1           BiocGenerics_0.14.0      
 [9] BiocInstaller_1.18.3      sva_3.14.0                genefilter_1.50.0         mgcv_1.8-6               
[13] nlme_3.1-121             

OK solved this by filtering out genes with zero counts.
Thanks a lot for the help.