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bugs
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0
votes
11
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1.9k
views
limma::contrast.fit() potential bugs when weights from voom() included
bugs
limma
2.4 years ago
Zhenyu
• 0
0
votes
2
replies
1.9k
views
AffyBatch and ArrayExpress
arrayexpress
affy
bugs
updated 6.9 years ago by
James W. MacDonald
67k • written 6.9 years ago by
Ed Siefker
▴ 230
5
votes
16
replies
2.8k
views
GSVA package scores are opposite on mac and windows
GSVA
bug
gsva
bugs
updated 7.3 years ago by
Robert Castelo
★ 3.4k • written 7.3 years ago by
JasonL_Weirather
▴ 10
0
votes
1
reply
1.3k
views
bug in dba.overlap (dba.plotVenn)
DiffBind
bugs
updated 7.6 years ago by
Rory Stark
★ 5.2k • written 7.7 years ago by
jeremydt
• 0
2
votes
3
replies
1.7k
views
A bug of "seqlevels<-" on TxDb
txdb.hsapiens.ucsc.hg19.knowngene
seqlevels
bugs
updated 8.1 years ago by
Hervé Pagès
16k • written 8.1 years ago by
wcstcyx
▴ 30
5
votes
2
replies
1.5k
views
AnnotationHub: two broad peaks from same url are not the same
annotationhub
bugs
encode
bed
8.1 years ago
wcstcyx
▴ 30
0
votes
0
replies
1.2k
views
Bugs for impute package
bugs
impute
8.4 years ago
Shicheng Guo
• 0
0
votes
4
replies
1.9k
views
DESeq2 contrast cleaning problem
software error
bugs
deseq2
updated 9.0 years ago by
Michael Love
43k • written 9.0 years ago by
john.hu
• 0
0
votes
0
replies
1.6k
views
error: no slot of name "expressionFamily" for this object of class "CellDataSet"
monocle
bugs
9.2 years ago
wanghao1993333
• 0
0
votes
2
replies
1.8k
views
x-axis ticks are misaligned in ggbio tracks
ggbio
bugs
tracks
autoplot
10.0 years ago • updated 9.9 years ago
cooketho
• 0
4
votes
3
replies
1.7k
views
arrayQualityMetrics error with one color array and log transform
arrayqualitymetrics
bugs
error
updated 10.2 years ago by
James W. MacDonald
67k • written 10.2 years ago by
daugherty_a
• 0
0
votes
4
replies
2.2k
views
DESeq2 more differentially expressed genes
Bugs
deseq2
updated 10.3 years ago by
Michael Love
43k • written 10.3 years ago by
lmf.bill@gmail.com
▴ 10
0
votes
0
replies
1.6k
views
ggbio() + geom_alignment has stopped working
Bugs
ggbio
10.3 years ago
Anne Deslattes Mays
▴ 30
13 results • Page
1 of 1
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Replies
Comment: How to sort negative log2FC or FC in RNAseq for GSEA?
by
QN
▴ 10
Thank you ATpoint for your response! In the result of GSEA, like you indicated, there will be gene sets that have positive NES and gene se…
Comment: EdgeR Biological CVs
by
ATpoint
★ 4.6k
"Joseph" is a spam bot...
Answer: How to sort negative log2FC or FC in RNAseq for GSEA?
by
ATpoint
★ 4.6k
GSEA asks whether there are general shifts in gene expression towards certain terms. Hence, you would not split your results tables but ord…
Comment: EdgeR Biological CVs
by
James
• 0
Thank you Gordon and Joseph. I presume question (1) would be answered by using a prior G0 of 0? For question (2), I was expecting a biolog…
Answer: EdgeR Biological CVs
by
Gordon Smyth
52k
I think your questions are answered by the published paper. You might also like to consult recent papers on edgeR by Yunshun Chen and Pedro…
Votes
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
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