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DGEList
•
reset
1
vote
4
replies
21k
views
edgeR: non-unique values when setting 'row.names' - but the row names are unique!!!
edgeR
row.names
DGEList
10.0 years ago
ccheung
• 0
3
votes
7
replies
7.2k
views
edgeR subsetting DGEList by column/sample
edger
subsetting
dgelist
updated 8.6 years ago by
Gordon Smyth
52k • written 8.6 years ago by
mnaymik
▴ 10
3
votes
3
replies
4.1k
views
Correct annotation of DGEList object from edgeR package regarding an RNA-Seq dataset
edger
DGEList
org.hs.eg.db
gene annotation
updated 3.4 years ago by
IIart.hubII
• 0 • written 7.2 years ago by
svlachavas
▴ 840
2
votes
4
replies
3.7k
views
Filtering DGEList object in edgeR
DGElist
filter
edgeR
updated 7.6 years ago by
Gordon Smyth
52k • written 7.6 years ago by
alakatos
▴ 130
0
votes
2
replies
3.6k
views
Design of 'group' object in DGElist function
egder
dgelist
group
rnaseq
updated 7.3 years ago by
Aaron Lun
★ 28k • written 7.3 years ago by
fawazfebin
▴ 60
4
votes
6
replies
2.9k
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 8.5 years ago by
Steve Lianoglou
★ 13k • written 8.5 years ago by
benedict.ng
▴ 30
0
votes
1
reply
2.5k
views
DGEList remove/exclude rows with entrezgene = 'NA'
edger
dgelist
NA
egsea
updated 7.0 years ago by
Gordon Smyth
52k • written 7.0 years ago by
belmore
• 0
1
vote
4
replies
2.5k
views
edgeR/DGEList add assays to a DGEList like in SummarizedExperiment
edgeR
summarizedexperiment
dgelist
6.8 years ago
aljoscha.leusmann
• 0
0
votes
2
replies
2.2k
views
create DGElist Object
edger
DGElist
updated 5.9 years ago by
Gordon Smyth
52k • written 5.9 years ago by
naser.sadri
• 0
0
votes
4
replies
2.0k
views
Error in RnaSeqGeneEdgeRQL
dgelist
edger
RnaSeqGeneEdgeRQL
updated 6.5 years ago by
Gordon Smyth
52k • written 6.5 years ago by
Kevin
• 0
0
votes
0
replies
1.1k
views
Using log2FC distance matrix in Boot.Phylo to create bootstrapped trees
tree
bootstrap
dgelist
plotmds
6.9 years ago
Larry K.
• 0
1
vote
1
reply
1.1k
views
Optimal edgeR design for a single-factor experiment
factors
edgeR
setup
DGELIst
updated 3.7 years ago by
Gordon Smyth
52k • written 3.7 years ago by
Alex
• 0
2
votes
2
replies
825
views
Inccorect group number in DGEList
edgeR
Bioconductor
Dseq2
dgelist
updated 2.1 years ago by
Gordon Smyth
52k • written 2.1 years ago by
Fiona
• 0
0
votes
2
replies
446
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
10 months ago
prity6459
• 0
14 results • Page
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Comment: For some reason I can't update BiocManager to 3.20
by
shepherl
4.1k
interesting. it could be since this is not your installation that it was installed by an admin that you do not have access to perform this…
Comment: Overcoming confounding in batch effect correction
by
ATpoint
★ 4.6k
Hi, this is not related to Bioconductor directly. And no, you cannot correct anything because in your own batch you only have a single samp…
Comment: MEDIPS - error using MEDIPS.CpGenrich
by
sg
• 0
I have the same error when I use 22 chrs with the paramenters chr.select: Error in h(simpleError(msg, call)) : error in evaluating the …
Comment: Overcoming confounding in batch effect correction
by
mimi
• 0
https://www.bioconductor.org/packages/release/BiocViews.html#___BiologicalQuestion
Comment: GSVA on RNAseq data
by
Robert Castelo
★ 3.4k
Hi Bob, I have not investigated whether a particular unit of expression works better than others, but using logTPM or logCPM units of expr…
Votes
Overcoming confounding in batch effect correction
Answer: Standardization of rlog transformed counts before PCA
Answer: Standardization of rlog transformed counts before PCA
Answer: Standardization of rlog transformed counts before PCA
Answer: Standardization of rlog transformed counts before PCA
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