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GSEABase
•
reset
2
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796
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fgsea stuck in an infinite loop in the middle of the run
GSEABase
fgsea
msigdb
GeneSetEnrichment
5 months ago
Assa Yeroslaviz
★ 1.5k
0
votes
2
replies
429
views
Problem finding certain variables when importing a public database GSE73103
GSEABase
GenomicDistributionsData
9 months ago
Yveto
• 0
0
votes
1
reply
262
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Problems with GSEA
GSEABase
updated 24 days ago by
Guido Hooiveld
★ 4.1k • written 24 days ago by
Sidra.Gull
• 0
3 results • Page
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Answer: To count or not to count multi-overlapping reads?
by
Gordon Smyth
52k
> How does it handle reads that map to a gene that is located in a region that also has another gene but on the alternate strand? Overlapp…
Comment: Weird p-values using DESeq2?
by
ATpoint
★ 4.7k
This does not look like normalized counts but raw counts. Consider using `counts(dds, normalized = TRUE)` or the output of `normTransform()…
Answer: Weird p-values using DESeq2?
by
Wolfgang Huber
★ 13k
Dear Ingrid, thank you for asking. Can you provide the input count matrix (you can "pseudonymize" the biological conditions and the gene n…
Comment: How to visualize these pathways using pathview
by
ingrid.h
• 0
Yes I have seen it, thanks.
Comment: Store Matrix in DataFrame Cell
by
Dario Strbenac
★ 1.6k
It does not appear to work. > DataFrame(name = "test", value = list(matrix(1:4, ncol = 2))) DataFrame with 2 rows and 3 columns …
Votes
A: Fraction count for multi mapping reads; how to generate input file for Deseq2 fo
Comment: Weird p-values using DESeq2?
Comment: Overcoming confounding in batch effect correction
Answer: Store Matrix in DataFrame Cell
Answer: enrichGOgradient color change
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