User: Samuel

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Samuel0
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Posts by Samuel

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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 2 days ago by Samuel0 • updated 2 days ago by Gordon Smyth38k
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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 6 days 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 16 days ago by Samuel0

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