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DGEList
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0
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2
replies
771
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How to make DGEList and design matrix by edgeR package
DGEList
edgeR
22 months ago
prity6459
• 0
2
votes
2
replies
1.1k
views
Inccorect group number in DGEList
edgeR
Bioconductor
Dseq2
dgelist
updated 3.2 years ago by
Gordon Smyth
53k • written 3.2 years ago by
Fiona
• 0
1
vote
1
reply
1.5k
views
Optimal edgeR design for a single-factor experiment
factors
edgeR
setup
DGELIst
updated 4.8 years ago by
Gordon Smyth
53k • written 4.8 years ago by
Alex
• 0
0
votes
2
replies
2.6k
views
create DGElist Object
edger
DGElist
updated 6.9 years ago by
Gordon Smyth
53k • written 6.9 years ago by
naser.sadri
• 0
0
votes
4
replies
2.3k
views
Error in RnaSeqGeneEdgeRQL
dgelist
edger
RnaSeqGeneEdgeRQL
updated 7.6 years ago by
Gordon Smyth
53k • written 7.6 years ago by
Kevin
• 0
1
vote
4
replies
3.1k
views
edgeR/DGEList add assays to a DGEList like in SummarizedExperiment
edgeR
summarizedexperiment
dgelist
7.9 years ago
aljoscha.leusmann
• 0
0
votes
0
replies
1.4k
views
Using log2FC distance matrix in Boot.Phylo to create bootstrapped trees
tree
bootstrap
dgelist
plotmds
8.0 years ago
Larry K.
• 0
0
votes
1
reply
2.9k
views
DGEList remove/exclude rows with entrezgene = 'NA'
edger
dgelist
NA
egsea
updated 8.0 years ago by
Gordon Smyth
53k • written 8.0 years ago by
belmore
• 0
3
votes
3
replies
4.6k
views
Correct annotation of DGEList object from edgeR package regarding an RNA-Seq dataset
edger
DGEList
org.hs.eg.db
gene annotation
updated 4.4 years ago by
IIart.hubII
• 0 • written 8.2 years ago by
svlachavas
▴ 840
0
votes
2
replies
3.9k
views
Design of 'group' object in DGElist function
egder
dgelist
group
rnaseq
updated 8.3 years ago by
Aaron Lun
★ 29k • written 8.3 years ago by
fawazfebin
▴ 60
2
votes
4
replies
4.3k
views
Filtering DGEList object in edgeR
DGElist
filter
edgeR
updated 8.6 years ago by
Gordon Smyth
53k • written 8.6 years ago by
alakatos
▴ 130
3
votes
6
replies
3.4k
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 9.5 years ago by
Steve Lianoglou
★ 13k • written 9.5 years ago by
benedict.ng
▴ 20
3
votes
7
replies
7.9k
views
edgeR subsetting DGEList by column/sample
edger
subsetting
dgelist
updated 9.6 years ago by
Gordon Smyth
53k • written 9.6 years ago by
mnaymik
▴ 10
1
vote
4
replies
23k
views
edgeR: non-unique values when setting 'row.names' - but the row names are unique!!!
edgeR
row.names
DGEList
11.1 years ago • updated 11.0 years ago
ccheung
• 0
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Answer: Issue loading and downloading Bioconductor 3.22 packages after update
by
James W. MacDonald
68k
As Robert and ATpoint have mentioned, you need to allow more time to download a large file like this. ``` > options(timeout = 5e5) > l…
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
by
Robert Castelo
★ 3.4k
Hi, the package you refer to is not called `SNPlocs.HSapiens.dbSNP155.GRCh38`, but `SNPlocs.Hsapiens.dbSNP155.GRCh38`, note the lowercase l…
Comment: Issue loading and downloading Bioconductor 3.22 packages after update
by
ATpoint
★ 5.0k
"Breaks" needs a more detailed explanation, together with code and error messages. Can you confirm it's not just the R download timeout aft…
Comment: Reproducibility of code in various Bioconductor versions
by
strawberry3
• 0
Thank you for advice! I have updated Bioconductor to the newest one, but now some of my commands don't work anymore, and I cannot download …
Answer: Reproducibility of code in various Bioconductor versions
by
Gordon Smyth
53k
I'm not familiar with the packages you mention, but the whole reason why Bioconductor has versions is that code and annotation change. Code…
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Answer: Question on processing compound protein groups in limpa
Answer: Correct usage of limpa for protein input
Answer: Correct usage of limpa for protein input
Answer: Correct usage of limpa for protein input
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