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DGElist
•
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0
votes
2
replies
129
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
15 days ago
prity6459
• 0
2
votes
2
replies
614
views
Inccorect group number in DGEList
edgeR
Bioconductor
Dseq2
dgelist
updated 16 months ago by
Gordon Smyth
50k • written 16 months ago by
Fiona
• 0
1
vote
1
reply
838
views
Optimal edgeR design for a single-factor experiment
factors
edgeR
setup
DGELIst
updated 3.0 years ago by
Gordon Smyth
50k • written 3.0 years ago by
Alex
• 0
0
votes
2
replies
1.7k
views
create DGElist Object
edger
DGElist
updated 5.1 years ago by
Gordon Smyth
50k • written 5.1 years ago by
naser.sadri
• 0
0
votes
4
replies
1.7k
views
Error in RnaSeqGeneEdgeRQL
dgelist
edger
RnaSeqGeneEdgeRQL
updated 5.8 years ago by
Gordon Smyth
50k • written 5.8 years ago by
Kevin
• 0
1
vote
4
replies
2.0k
views
edgeR/DGEList add assays to a DGEList like in SummarizedExperiment
edgeR
summarizedexperiment
dgelist
6.0 years ago
aljoscha.leusmann
• 0
0
votes
0
replies
924
views
Using log2FC distance matrix in Boot.Phylo to create bootstrapped trees
tree
bootstrap
dgelist
plotmds
6.1 years ago
Larry K.
• 0
0
votes
1
reply
2.2k
views
DGEList remove/exclude rows with entrezgene = 'NA'
edger
dgelist
NA
egsea
updated 6.2 years ago by
Gordon Smyth
50k • written 6.2 years ago by
belmore
• 0
3
votes
3
replies
3.6k
views
Correct annotation of DGEList object from edgeR package regarding an RNA-Seq dataset
edger
DGEList
org.hs.eg.db
gene annotation
updated 2.6 years ago by
IIart.hubII
• 0 • written 6.4 years ago by
svlachavas
▴ 830
0
votes
2
replies
3.0k
views
Design of 'group' object in DGElist function
egder
dgelist
group
rnaseq
updated 6.5 years ago by
Aaron Lun
★ 28k • written 6.5 years ago by
fawazfebin
▴ 60
2
votes
4
replies
3.2k
views
Filtering DGEList object in edgeR
DGElist
filter
edgeR
updated 6.8 years ago by
Gordon Smyth
50k • written 6.8 years ago by
alakatos
▴ 130
3
votes
6
replies
2.5k
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 7.7 years ago by
Steve Lianoglou
★ 13k • written 7.7 years ago by
benedict.ng
▴ 20
3
votes
7
replies
6.6k
views
edgeR subsetting DGEList by column/sample
edger
subsetting
dgelist
updated 7.8 years ago by
Gordon Smyth
50k • written 7.8 years ago by
mnaymik
▴ 10
1
vote
4
replies
20k
views
edgeR: non-unique values when setting 'row.names' - but the row names are unique!!!
edgeR
row.names
DGEList
9.2 years ago
ccheung
• 0
14 results • Page
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Recent ...
Replies
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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