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1
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4
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22k
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edgeR: non-unique values when setting 'row.names' - but the row names are unique!!!
edgeR
row.names
DGEList
10.3 years ago
ccheung
• 0
3
votes
7
replies
7.5k
views
edgeR subsetting DGEList by column/sample
edger
subsetting
dgelist
updated 8.8 years ago by
Gordon Smyth
52k • written 8.8 years ago by
mnaymik
▴ 10
3
votes
3
replies
4.3k
views
Correct annotation of DGEList object from edgeR package regarding an RNA-Seq dataset
edger
DGEList
org.hs.eg.db
gene annotation
updated 3.6 years ago by
IIart.hubII
• 0 • written 7.4 years ago by
svlachavas
▴ 840
2
votes
4
replies
3.9k
views
Filtering DGEList object in edgeR
DGElist
filter
edgeR
updated 7.9 years ago by
Gordon Smyth
52k • written 7.9 years ago by
alakatos
▴ 130
0
votes
2
replies
3.7k
views
Design of 'group' object in DGElist function
egder
dgelist
group
rnaseq
updated 7.5 years ago by
Aaron Lun
★ 28k • written 7.5 years ago by
fawazfebin
▴ 60
4
votes
6
replies
3.0k
views
How to carry out differential gene expression starting with a table of TMM normalised values without access to the raw reads?
edger
raw reads
TMM normalised values
DGEList
differential gene expression
updated 8.8 years ago by
Steve Lianoglou
★ 13k • written 8.8 years ago by
benedict.ng
▴ 30
1
vote
4
replies
2.7k
views
edgeR/DGEList add assays to a DGEList like in SummarizedExperiment
edgeR
summarizedexperiment
dgelist
7.1 years ago
aljoscha.leusmann
• 0
0
votes
1
reply
2.6k
views
DGEList remove/exclude rows with entrezgene = 'NA'
edger
dgelist
NA
egsea
updated 7.2 years ago by
Gordon Smyth
52k • written 7.2 years ago by
belmore
• 0
0
votes
2
replies
2.3k
views
create DGElist Object
edger
DGElist
updated 6.1 years ago by
Gordon Smyth
52k • written 6.1 years ago by
naser.sadri
• 0
0
votes
4
replies
2.1k
views
Error in RnaSeqGeneEdgeRQL
dgelist
edger
RnaSeqGeneEdgeRQL
updated 6.8 years ago by
Gordon Smyth
52k • written 6.8 years ago by
Kevin
• 0
1
vote
1
reply
1.2k
views
Optimal edgeR design for a single-factor experiment
factors
edgeR
setup
DGELIst
updated 4.0 years ago by
Gordon Smyth
52k • written 4.0 years ago by
Alex
• 0
0
votes
0
replies
1.2k
views
Using log2FC distance matrix in Boot.Phylo to create bootstrapped trees
tree
bootstrap
dgelist
plotmds
7.2 years ago
Larry K.
• 0
2
votes
2
replies
877
views
Inccorect group number in DGEList
edgeR
Bioconductor
Dseq2
dgelist
updated 2.4 years ago by
Gordon Smyth
52k • written 2.4 years ago by
Fiona
• 0
0
votes
2
replies
531
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
13 months ago
prity6459
• 0
14 results • Page
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Comment: Check removeBatchEffect effectiveness
by
massimo
• 0
Sorry for the delay, here it is my code which displays the warning message: Normalization: countsdge <- DGEList(counts, timepoint, ge…
Answer: WGCNA coupled with differential expression analysis: question about baseline mod
by
phylliskeller162
• 0
My reflexes are challenged every time I play [Dinosaur Game][1]! [1]: https://dinosaur-game.io
Answer: blockwiseModule crashes in the end and doesn't generate modules
by
phylliskeller162
• 0
Crave adrenaline, music, and pixel-perfect jumps? [Geometry Dash][1] delivers it all in one pulse-pounding ride! [1]: https://geomet…
Comment: How to extract coordinates of mismatches from a BAM file lodaded in as a GAlignm
by
Charles
• 0
I am trying this but it is slow. ``` aln2mismatches <- function (gal) { gr <- GRanges(gal) irl <- cigarRangesAlongReferenceSpace(cigar…
Answer: DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change
by
James W. MacDonald
68k
Yes, you can simply flip the sign of the logFC to reverse the direction of the comparison.
Votes
Comment: Heatmap of a transformed deseq object with pheatmap
DESeq2: Question about the alpha in summary() and results()
Comment: How to load scRNA-seq data from GEO
limma correction for tumor purity
limma correction for tumor purity
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