Question: How to filter tximport output for edgeR?
0
3.0 years ago by
Peter0
United Kingdom
Peter0 wrote:

The tximport vignette describes the following steps for using the data with edgeR:

https://github.com/mikelove/tximport/blob/master/vignettes/tximport.md

library(edgeR)
cts <- txi$counts normMat <- txi$length
normMat <- normMat/exp(rowMeans(log(normMat)))
library(edgeR)
o <- log(calcNormFactors(cts/normMat)) + log(colSums(cts/normMat))
y <- DGEList(cts)
y$offset <- t(t(log(normMat)) + o) # y is now ready for estimate dispersion functions see edgeR User's Guide How should I modify the data to filter non-expressed genes before calculating normalization factors? (e.g. cpm>2 in at least 3 samples) edger rna-seq salmon tximport • 794 views ADD COMMENTlink modified 3.0 years ago by Michael Love25k • written 3.0 years ago by Peter0 Answer: How to filter tximport output for edgeR? 0 3.0 years ago by Michael Love25k United States Michael Love25k wrote: You should be able to adapt the cpm filtering code from the edgeR User Guide, no? y is a DGEList, with normalization factors already calculated. Can you be more specific about your question? ADD COMMENTlink written 3.0 years ago by Michael Love25k Using the guide then it would look like this: ... y <- DGEList(cts) keep <- rowSums(cpm(y) > 2) >= 3 y <- y[keep, , keep.lib.sizes=FALSE] But then I guess I need to recalculate the normalization factors, and also was not sure about the offset calculation. y$offset <- t(t(log(normMat)) + o)

Not that important as I can use countsFromAbundance="lengthScaledTPM" or "scaledTPM" and then use counts, but wanted to compare results from the two approaches.

Maybe one of the edgeR authors can say more on this, but you could just do keep.lib.sizes=TRUE for comparison with the countsFromAbundance approach.

Hello, excuse me, I am a bit new in R. I have used this command y\$offset <- t(t(log(normMat)) + o) to make a box plot. what should be written as vertical axis title and horizontal axis title of box plot? may I also make a heatmap clustering for that? thanks in advance

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This isn’t a tximport question. Maybe consult related papers and workflows for background. edgeR has workflows you can consult.