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limma::contrast.fit() potential bugs when weights from voom() included
bugs
limma
2.3 years ago
Zhenyu
• 0
0
votes
2
replies
1.8k
views
AffyBatch and ArrayExpress
arrayexpress
affy
bugs
updated 6.8 years ago by
James W. MacDonald
67k • written 6.8 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 7.2 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 7.6 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
8.3 years ago
Shicheng Guo
• 0
0
votes
4
replies
1.9k
views
DESeq2 contrast cleaning problem
software error
bugs
deseq2
updated 8.9 years ago by
Michael Love
43k • written 8.9 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
9.1 years ago
wanghao1993333
• 0
0
votes
2
replies
1.8k
views
x-axis ticks are misaligned in ggbio tracks
ggbio
bugs
tracks
autoplot
9.9 years ago
cooketho
• 0
4
votes
3
replies
1.6k
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
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Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis
by
Andre
• 0
Thank you. What is the difference between setting robust=TRUE in glmQLFit and estimateGLMRobustDisp? The paper i mentioned in the post used…
Comment: PCA of different bacterial species
by
Jeremy
• 0
Your approach of using ~2500 single-copy orthologs and normalizing with VST or rlog for PCA is valid for exploring general clustering [pap…
Comment: RnBeads::combine() - error?
by
Urotree
• 0
pheno <- rnb.set.arrays@pheno # Phenotypic data sites <- rnb.set.arrays@sites # CpG site definitions (data.frame) meth <- rnb.set…
Comment: RnBeads::combine() - error?
by
Urotree
• 0
![enter image description here][1] [1]: /media/images/40d9778d-b044-4405-9b3d-2ba835f6 Hi, after I convert to RnBiseqSet, it shows "All…
Comment: RnBeads::combine() - error?
by
Urotree
• 0
rnb.set.biseq <- RnBiseqSet( pheno = pheno, sites = sites, meth = meth, covg = NULL, # This can be NULL if coverage …
Votes
Answer: Incorporating Salmon offset matrix into Wilcoxon DEG analysis
scater/scran with TPMs from Salmon - counts?
A: Full length single-cell RNA-seq - tximport output for downstream analysis
Answer: Understanding tximport working with salmon outputs
Answer: enrichGOgradient color change
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