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import.bw
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R/Rstudio: using rtracklayer to import bigwig files from http works with MacOS but not with Windows
import.bw
rtracklayer
Windows
http
2.5 years ago • updated 2.4 years ago
sla
• 0
2
votes
4
replies
1.1k
views
default behaviour of import.bw
import.bw
rtracklayer
2.5 years ago
Yixin
• 0
1
vote
5
replies
4.0k
views
RStudio vs R: using rtracklayer to import bigwig files from http works in R but not in RStudio.
import.bw
rtracklayer
http
RStudio
updated 3.4 years ago by
Michael Lawrence
★ 11k • written 3.4 years ago by
Søren
• 0
4
votes
1
reply
1.1k
views
What's the recommended way to overwrite the seqinfo of a GRanges?
GRanges
seqinfo
import.bw
BigWigFile
rtracklayer
updated 5.2 years ago by
Michael Lawrence
★ 11k • written 5.2 years ago by
maltethodberg
▴ 180
3
votes
2
replies
970
views
does import.bw with the selection argument take into account strand?
rtracklayer
import.bw
updated 7.6 years ago by
Michael Lawrence
★ 11k • written 7.6 years ago by
maltethodberg
▴ 180
0
votes
6
replies
2.4k
views
Problem with importing bigwig files generated in galaxy into R
import.bw
rtracklayer
updated 9.0 years ago by
Michael Lawrence
★ 11k • written 9.0 years ago by
d r
▴ 150
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Comment: Help with running egsea()
by
Chris
• 0
I tried egsea.ma and got this error: gsa = egsea.ma(numeric_matrix, vector_group, probe_annotation, contrasts = contrast_matrix, gs.an…
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
angelathuynh5
• 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
by
James W. MacDonald
65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Votes
Answer: confused with tximport counts abundance using salmon input
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
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