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dgelist
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0
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2
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723
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How to make DGEList and design matrix by edgeR package
DGEList
edgeR
19 months ago
prity6459
• 0
2
votes
2
replies
1.0k
views
Inccorect group number in DGEList
edgeR
Bioconductor
Dseq2
dgelist
updated 3.0 years ago by
Gordon Smyth
53k • written 3.0 years ago by
Fiona
• 0
1
vote
1
reply
1.4k
views
Optimal edgeR design for a single-factor experiment
factors
edgeR
setup
DGELIst
updated 4.6 years ago by
Gordon Smyth
53k • written 4.6 years ago by
Alex
• 0
0
votes
2
replies
2.5k
views
create DGElist Object
edger
DGElist
updated 6.7 years ago by
Gordon Smyth
53k • written 6.7 years ago by
naser.sadri
• 0
0
votes
4
replies
2.2k
views
Error in RnaSeqGeneEdgeRQL
dgelist
edger
RnaSeqGeneEdgeRQL
updated 7.4 years ago by
Gordon Smyth
53k • written 7.4 years ago by
Kevin
• 0
1
vote
4
replies
3.0k
views
edgeR/DGEList add assays to a DGEList like in SummarizedExperiment
edgeR
summarizedexperiment
dgelist
7.6 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
7.7 years ago
Larry K.
• 0
0
votes
1
reply
2.8k
views
DGEList remove/exclude rows with entrezgene = 'NA'
edger
dgelist
NA
egsea
updated 7.8 years ago by
Gordon Smyth
53k • written 7.8 years ago by
belmore
• 0
3
votes
3
replies
4.5k
views
Correct annotation of DGEList object from edgeR package regarding an RNA-Seq dataset
edger
DGEList
org.hs.eg.db
gene annotation
updated 4.2 years ago by
IIart.hubII
• 0 • written 8.0 years ago by
svlachavas
▴ 840
0
votes
2
replies
3.9k
views
Design of 'group' object in DGElist function
egder
dgelist
group
rnaseq
updated 8.1 years ago by
Aaron Lun
★ 29k • written 8.1 years ago by
fawazfebin
▴ 60
2
votes
4
replies
4.2k
views
Filtering DGEList object in edgeR
DGElist
filter
edgeR
updated 8.4 years ago by
Gordon Smyth
53k • written 8.4 years ago by
alakatos
▴ 130
4
votes
6
replies
3.3k
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 9.3 years ago by
Steve Lianoglou
★ 13k • written 9.3 years ago by
benedict.ng
▴ 30
3
votes
7
replies
7.7k
views
edgeR subsetting DGEList by column/sample
edger
subsetting
dgelist
updated 9.4 years ago by
Gordon Smyth
53k • written 9.4 years ago by
mnaymik
▴ 10
1
vote
4
replies
22k
views
edgeR: non-unique values when setting 'row.names' - but the row names are unique!!!
edgeR
row.names
DGEList
10.8 years ago
ccheung
• 0
14 results • Page
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Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes
by
Erik Wright
▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
by
Michael Love
43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA
by
Gordon Smyth
53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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