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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
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
1.6k
views
DESeq2 contrast cleaning problem
software error
bugs
deseq2
updated 8.2 years ago by
Michael Love
41k • written 8.2 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
1.4k
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 6.9 years ago by
jeremydt
• 0
0
votes
2
replies
1.6k
views
AffyBatch and ArrayExpress
arrayexpress
affy
bugs
updated 6.1 years ago by
James W. MacDonald
65k • written 6.1 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
9.2 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
1.4k
views
error: no slot of name "expressionFamily" for this object of class "CellDataSet"
monocle
bugs
8.4 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
1 of 1
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Replies
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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