User: Samuel

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Samuel0
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Posts by Samuel

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Modelling a multiplicative batch effect with DESeq2
... As far as I understand, The process by which DESeq2 models a batch effect is close to : Subtracting the arithmetic mean of the batches' expression values from the genes, on a per-gene basis. Is it possible in DESeq2 instead of modelling only an additive batch effect, to model a multiplicative one ...
deseq2 combat batch-effects written 15 days ago by Samuel0 • updated 14 days ago by Michael Love25k
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What to do when a bug is found in a BioConductor package (Glimma)
... As far as I can tell, I have found a bug in Glimma. The following code library(Glimma) DE <- as.data.frame(cbind(202197.7, -1.410116), byrow=T) colnames(DE) <- c("baseMean", "log2FoldChange") DE$sig <- 1 glMDPlot(x=DE, xval="baseMean", yval="log2Fol ...
software error glimma written 9 weeks ago by Samuel0 • updated 9 weeks ago by Gordon Smyth39k
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The correct specification of the model matrix to ComBat
... When using the ComBat function for batch correction, what is the difference between the following two specifications of the matrix model : mod <- model.matrix(~1, dat=colData) mod <- model.matrix(~ ConditionOfInterest, dat=colData) When calling ComBat(dat=expressionMatrix, batc ...
sva combat written 9 weeks ago by Samuel0
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Comment: C: Can NanoString data be analyzed using DESeq2?
... DESeq assumes most genes are not DE. In Nanostring, as far as I understand, only genes that are expected to change are inspected (besides the housekeeping genes). Is this DESeq assumption necessary only for the normalization step? If it is necessary for other steps in the process, it's hard to unde ...
written 11 weeks ago by Samuel0

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