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DGEList
•
reset
0
votes
2
replies
238
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
3 months ago
prity6459
• 0
2
votes
2
replies
682
views
Inccorect group number in DGEList
edgeR
Bioconductor
Dseq2
dgelist
updated 19 months ago by
Gordon Smyth
51k • written 19 months ago by
Fiona
• 0
1
vote
1
reply
930
views
Optimal edgeR design for a single-factor experiment
factors
edgeR
setup
DGELIst
updated 3.2 years ago by
Gordon Smyth
51k • written 3.2 years ago by
Alex
• 0
0
votes
2
replies
1.9k
views
create DGElist Object
edger
DGElist
updated 5.3 years ago by
Gordon Smyth
51k • written 5.3 years ago by
naser.sadri
• 0
0
votes
4
replies
1.8k
views
Error in RnaSeqGeneEdgeRQL
dgelist
edger
RnaSeqGeneEdgeRQL
updated 6.0 years ago by
Gordon Smyth
51k • written 6.0 years ago by
Kevin
• 0
1
vote
4
replies
2.2k
views
edgeR/DGEList add assays to a DGEList like in SummarizedExperiment
edgeR
summarizedexperiment
dgelist
6.3 years ago
aljoscha.leusmann
• 0
0
votes
0
replies
983
views
Using log2FC distance matrix in Boot.Phylo to create bootstrapped trees
tree
bootstrap
dgelist
plotmds
6.4 years ago
Larry K.
• 0
0
votes
1
reply
2.3k
views
DGEList remove/exclude rows with entrezgene = 'NA'
edger
dgelist
NA
egsea
updated 6.4 years ago by
Gordon Smyth
51k • written 6.4 years ago by
belmore
• 0
3
votes
3
replies
3.8k
views
Correct annotation of DGEList object from edgeR package regarding an RNA-Seq dataset
edger
DGEList
org.hs.eg.db
gene annotation
updated 2.8 years ago by
IIart.hubII
• 0 • written 6.7 years ago by
svlachavas
▴ 830
0
votes
2
replies
3.2k
views
Design of 'group' object in DGElist function
egder
dgelist
group
rnaseq
updated 6.7 years ago by
Aaron Lun
★ 28k • written 6.7 years ago by
fawazfebin
▴ 60
2
votes
4
replies
3.3k
views
Filtering DGEList object in edgeR
DGElist
filter
edgeR
updated 7.1 years ago by
Gordon Smyth
51k • written 7.1 years ago by
alakatos
▴ 130
3
votes
6
replies
2.6k
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 8.0 years ago by
Steve Lianoglou
★ 13k • written 8.0 years ago by
benedict.ng
▴ 20
3
votes
7
replies
6.8k
views
edgeR subsetting DGEList by column/sample
edger
subsetting
dgelist
updated 8.0 years ago by
Gordon Smyth
51k • written 8.0 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
9.5 years ago
ccheung
• 0
14 results • Page
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Replies
Answer: Validity of SingleR with very small bulk RNAseq reference
by
ATpoint
★ 4.2k
The vignette data are "large" because it is single-cell data and each cell is considered in this case a "replicate". With bulk RNA-seq you …
Answer: Plot PCA with ellipses using ggplot
by
ATpoint
★ 4.2k
This is rather a ggplot than DESeq2 question, please see for example https://stackoverflow.com/questions/49931681/error-too-few-points-to-c…
Comment: 'path' must be string
by
James W. MacDonald
66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string
by
cpierce2
• 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest
by
Robert
• 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
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ATpoint
★ 4.2k
Popular Question
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Lluís Revilla Sancho
▴ 730
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maltethodberg
▴ 180
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Michael Love
42k
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Leonardo Collado Torres
★ 1.1k
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