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Glimma
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5
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4
replies
1.4k
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Glimma Interactive plots for RNAseq
Glimma
R markdown
rnaseq
6.2 years ago
Aurora
▴ 20
0
votes
1
reply
827
views
Why does the Glimma package require R >= 3.4.0 ?
glimma
updated 6.1 years ago by
Shian Su
▴ 40 • written 6.1 years ago by
gil.hornung
• 0
1
vote
3
replies
1.5k
views
problem installing the Glimma package
glimma
6.1 years ago
omran.allatif
• 0
2
votes
2
replies
985
views
What to do when a bug is found in a BioConductor package (Glimma)
glimma
software error
updated 4.7 years ago by
Gordon Smyth
50k • written 4.7 years ago by
Sam
▴ 10
7
votes
6
replies
1.3k
views
BiocStyle::html_document does not render Glimma plots
Glimma
BiocStyle
updated 21 months ago by
Mike Smith
★ 6.5k • written 21 months ago by
neilzhao
▴ 30
1
vote
1
reply
476
views
Extracting the tophits from limma Volcanoplot and issue with geneIDs
limma
edgeR
Glimma
updated 16 months ago by
Gordon Smyth
50k • written 16 months ago by
Mohammad
• 0
1
vote
2
replies
1.0k
views
bug in Glimma - anno can't have T/F
Glimma
7.8 years ago
Jenny Drnevich
★ 2.0k
0
votes
2
replies
919
views
glimmaMA() produces blank plot if have annot column named "gene"
Glimma
updated 2.1 years ago by
Shian Su
▴ 40 • written 2.9 years ago by
Jenny Drnevich
★ 2.0k
0
votes
0
replies
1.1k
views
Glimma: Error: Length of groups must be equal to the number of columns in counts
Glimma
RNASeq
2.3 years ago
Jonas
• 0
0
votes
0
replies
521
views
Complex design in DESeq2 doesn't seem to be supported in Glimma
limma
Glimma
RNASeq
DESeq2
2.3 years ago
Jonas
• 0
10 results • Page
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Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
by
Michael Love
41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO
by
fernanda.backsouza
▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
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