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11
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1.5k
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limma::contrast.fit() potential bugs when weights from voom() included
bugs
limma
20 months ago • updated 19 months ago
Zhenyu
• 0
0
votes
4
replies
2.0k
views
DESeq2 more differentially expressed genes
Bugs
deseq2
updated 9.6 years ago by
Michael Love
41k • written 9.6 years ago by
lmf.bill@gmail.com
▴ 10
5
votes
16
replies
2.3k
views
GSVA package scores are opposite on mac and windows
GSVA
bug
gsva
bugs
updated 6.6 years ago by
Robert Castelo
★ 3.3k • written 6.6 years ago by
JasonL_Weirather
▴ 10
0
votes
4
replies
1.7k
views
DESeq2 contrast cleaning problem
software error
bugs
deseq2
updated 8.3 years ago by
Michael Love
41k • written 8.3 years ago by
john.hu
• 0
4
votes
3
replies
1.5k
views
arrayQualityMetrics error with one color array and log transform
arrayqualitymetrics
bugs
error
updated 9.5 years ago by
James W. MacDonald
65k • written 9.5 years ago by
daugherty_a
• 0
5
votes
2
replies
1.2k
views
AnnotationHub: two broad peaks from same url are not the same
annotationhub
bugs
encode
bed
7.4 years ago
wcstcyx
▴ 30
2
votes
3
replies
1.5k
views
A bug of "seqlevels<-" on TxDb
txdb.hsapiens.ucsc.hg19.knowngene
seqlevels
bugs
updated 7.4 years ago by
Hervé Pagès
16k • written 7.4 years ago by
wcstcyx
▴ 30
0
votes
1
reply
1.1k
views
bug in dba.overlap (dba.plotVenn)
DiffBind
bugs
updated 6.9 years ago by
Rory Stark
★ 5.2k • written 7.0 years ago by
jeremydt
• 0
0
votes
2
replies
1.6k
views
AffyBatch and ArrayExpress
arrayexpress
affy
bugs
updated 6.2 years ago by
James W. MacDonald
65k • written 6.2 years ago by
Ed Siefker
▴ 230
0
votes
2
replies
1.6k
views
x-axis ticks are misaligned in ggbio tracks
ggbio
bugs
tracks
autoplot
9.3 years ago • updated 9.2 years ago
cooketho
• 0
0
votes
0
replies
1.1k
views
Bugs for impute package
bugs
impute
7.6 years ago
Shicheng Guo
• 0
0
votes
0
replies
1.5k
views
error: no slot of name "expressionFamily" for this object of class "CellDataSet"
monocle
bugs
8.5 years ago
wanghao1993333
• 0
0
votes
0
replies
1.4k
views
ggbio() + geom_alignment has stopped working
Bugs
ggbio
9.6 years ago
Anne Deslattes Mays
▴ 30
13 results • Page
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Recent ...
Replies
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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