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diffSplice
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1
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837
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Selecting pairs of exons from differentially spliced genes
diffSplice
limma
2.7 years ago
jamie.gearing
▴ 60
2
votes
3
replies
756
views
Reasoning behind weighting of of exon expression values in limma diffSplice function
limma
diffSplice
updated 3.6 years ago by
Gordon Smyth
50k • written 3.6 years ago by
gerberst
• 0
1
vote
3
replies
1.4k
views
Use of RMA to get exon-level summaries for HTA 2.0
differential exon usage
exon array analysis
annotation
hta2.0
diffsplice
updated 6.6 years ago by
James W. MacDonald
65k • written 6.6 years ago by
relathman
▴ 20
5
votes
2
replies
1.2k
views
Warning messages from diffSplice in Limma
limma
diffSplice
updated 7.0 years ago by
Gordon Smyth
50k • written 7.0 years ago by
willj
▴ 30
15
votes
6
replies
3.2k
views
Reference paper or resource for limma::diffSplice and edgeR::diffSpliceDGE methods?
edgeR
limma
diffSplice
DEXSeq
updated 7.7 years ago by
Charity Law
▴ 90 • written 7.7 years ago by
maltethodberg
▴ 170
0
votes
0
replies
1.1k
views
plotSplice plotting only exons passing the filter makes the plot loose gene structure
limma
diffSplice
plotSplice
exons
annotation
8.7 years ago
Jose M Garcia Manteiga
▴ 310
6 results • Page
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Comment: Reproducibility issue with scran together with lapply and BiocParallel
by
ATpoint
★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel
by
Aaron Lun
★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio
by
Aaliya
• 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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