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DGElist
•
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0
votes
2
replies
415
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
8 months ago
prity6459
• 0
2
votes
2
replies
807
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
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
0
votes
2
replies
2.1k
views
create DGElist Object
edger
DGElist
updated 5.8 years ago by
Gordon Smyth
52k • written 5.8 years ago by
naser.sadri
• 0
0
votes
4
replies
1.9k
views
Error in RnaSeqGeneEdgeRQL
dgelist
edger
RnaSeqGeneEdgeRQL
updated 6.4 years ago by
Gordon Smyth
52k • written 6.4 years ago by
Kevin
• 0
1
vote
4
replies
2.5k
views
edgeR/DGEList add assays to a DGEList like in SummarizedExperiment
edgeR
summarizedexperiment
dgelist
6.7 years ago
aljoscha.leusmann
• 0
0
votes
0
replies
1.1k
views
Using log2FC distance matrix in Boot.Phylo to create bootstrapped trees
tree
bootstrap
dgelist
plotmds
6.8 years ago
Larry K.
• 0
0
votes
1
reply
2.5k
views
DGEList remove/exclude rows with entrezgene = 'NA'
edger
dgelist
NA
egsea
updated 6.9 years ago by
Gordon Smyth
52k • written 6.9 years ago by
belmore
• 0
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 3.3 years ago by
IIart.hubII
• 0 • written 7.1 years ago by
svlachavas
▴ 840
0
votes
2
replies
3.5k
views
Design of 'group' object in DGElist function
egder
dgelist
group
rnaseq
updated 7.2 years ago by
Aaron Lun
★ 28k • written 7.2 years ago by
fawazfebin
▴ 60
2
votes
4
replies
3.7k
views
Filtering DGEList object in edgeR
DGElist
filter
edgeR
updated 7.5 years ago by
Gordon Smyth
52k • written 7.5 years ago by
alakatos
▴ 130
4
votes
6
replies
2.8k
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 8.4 years ago by
Steve Lianoglou
★ 13k • written 8.4 years ago by
benedict.ng
▴ 30
3
votes
7
replies
7.2k
views
edgeR subsetting DGEList by column/sample
edger
subsetting
dgelist
updated 8.5 years ago by
Gordon Smyth
52k • written 8.5 years ago by
mnaymik
▴ 10
1
vote
4
replies
21k
views
edgeR: non-unique values when setting 'row.names' - but the row names are unique!!!
edgeR
row.names
DGEList
9.9 years ago
ccheung
• 0
14 results • Page
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Answer: promoters_txdb <- promoters(txdb, upstream = 2000) is not 2000
by
James W. MacDonald
67k
If you use `promoters` and do not provide an argument for something that has a default, you will get the default argument. Your last call t…
Comment: org.Hs.eg.db issue
by
k.panov
• 0
installed R on another PC, works perfectly. ergo, problem outside of R probably..... :-(
Comment: MBDseq analysis using qsea package
by
Lukas
▴ 20
Hi, I checked in with Matthias and here is his response: You need to indicate "samples": "The indices of the samples for which individu…
Comment: DESeq2 analysis with transcript counts
by
sindhuri
• 0
Thank you for the response. Currently I am using the R studio for analysis and Im running DESeq2 for analysis of the **transcript counts.ts…
Comment: iam not able to do retrive data using GEOquery R package
by
James W. MacDonald
67k
Another alternative is to use the `GEOmetadb` package ([vignette here)][1], which will allow you to make queries to identify GEO datasets t…
Votes
Answer: Is there any chance to solve "the model matrix is not full rank" in DESeq2?
Answer: Issue carrying out DiffBind Analysis at a predefined peak set
Answer: Differential variability modelling with vst() expression
Answer: Differential variability modelling with vst() expression
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
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