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Comment: filtering out lowly expressed genes by groups
by
James W. MacDonald
63k
You might want to filter first though.
```
fun <- function(deseqobj, contvec, cutoff) {
lildds <- dds[rowMeans(assays(deseqobj…
Answer: filtering out lowly expressed genes by groups
by
James W. MacDonald
63k
Something like
```
results(dds, c("condition","T0_unstim_CRWnP","T0_unstim_HC"))[rowMeans(assays(dds, "counts")[,colData(dds)$condition…
Comment: Representation of self-loops and the calculation of degrees
by
Vincent J. Carey, Jr.
6.7k
> packageVersion("graph")
[1] '1.79.2'
> gn <- graphNEL(nodes=c('A','B'), edgeL=list(A=c('A','B'), B=c('A')), edgemode='undirec…
Comment: filtering out lowly expressed genes by groups
by
sohail.mbio
▴
10
My question is how to avoid these DEGs? There are so many DEGs that are not actually expressed at T0. Is there any filter ?
my current code…
Answer: Why dbConnect GEOmetadb_demo.sqlite shows some information while dbConnect GEOme
by
James W. MacDonald
63k
The current `GEOmetadb.sqlite` file apparently has no entries for the `bioc_package` field. The table isn't empty however.
```
##
> z…
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