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DGEList
•
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0
votes
2
replies
363
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
6 months ago
prity6459
• 0
2
votes
2
replies
772
views
Inccorect group number in DGEList
edgeR
Bioconductor
Dseq2
dgelist
updated 23 months ago by
Gordon Smyth
51k • written 23 months ago by
Fiona
• 0
1
vote
1
reply
1.0k
views
Optimal edgeR design for a single-factor experiment
factors
edgeR
setup
DGELIst
updated 3.5 years ago by
Gordon Smyth
51k • written 3.5 years ago by
Alex
• 0
0
votes
2
replies
2.0k
views
create DGElist Object
edger
DGElist
updated 5.6 years ago by
Gordon Smyth
51k • written 5.6 years ago by
naser.sadri
• 0
0
votes
4
replies
1.9k
views
Error in RnaSeqGeneEdgeRQL
dgelist
edger
RnaSeqGeneEdgeRQL
updated 6.3 years ago by
Gordon Smyth
51k • written 6.3 years ago by
Kevin
• 0
1
vote
4
replies
2.4k
views
edgeR/DGEList add assays to a DGEList like in SummarizedExperiment
edgeR
summarizedexperiment
dgelist
6.6 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
6.7 years ago
Larry K.
• 0
0
votes
1
reply
2.4k
views
DGEList remove/exclude rows with entrezgene = 'NA'
edger
dgelist
NA
egsea
updated 6.7 years ago by
Gordon Smyth
51k • written 6.7 years ago by
belmore
• 0
3
votes
3
replies
4.0k
views
Correct annotation of DGEList object from edgeR package regarding an RNA-Seq dataset
edger
DGEList
org.hs.eg.db
gene annotation
updated 3.1 years ago by
IIart.hubII
• 0 • written 7.0 years ago by
svlachavas
▴ 830
0
votes
2
replies
3.4k
views
Design of 'group' object in DGElist function
egder
dgelist
group
rnaseq
updated 7.0 years ago by
Aaron Lun
★ 28k • written 7.0 years ago by
fawazfebin
▴ 60
2
votes
4
replies
3.6k
views
Filtering DGEList object in edgeR
DGElist
filter
edgeR
updated 7.4 years ago by
Gordon Smyth
51k • written 7.4 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 8.3 years ago by
Steve Lianoglou
★ 13k • written 8.3 years ago by
benedict.ng
▴ 30
3
votes
7
replies
7.1k
views
edgeR subsetting DGEList by column/sample
edger
subsetting
dgelist
updated 8.3 years ago by
Gordon Smyth
51k • written 8.3 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
9.8 years ago
ccheung
• 0
14 results • Page
1 of 1
Recent ...
Replies
Comment: Limma- Print-tip loess normalisation-printer layout information does not match M
by
dseauer
• 0
Thank you so much for all of your help! I really appreciate it!
Comment: Limma- Print-tip loess normalisation-printer layout information does not match M
by
Gordon Smyth
51k
Thanks for extra info, but be careful that the Bioconductor support site requires code to be an markdown format. Copying code with prompts …
Comment: Limma- Print-tip loess normalisation-printer layout information does not match M
by
dseauer
• 0
Thank you so much for your reply! I am sincerely sorry- of course I do not have multiple GAL files- just one- I meant gpr files! I am so so…
Comment: Is it possible to parallelise saveHDF5SummarizedExperiment
by
Stefano Mangiola
▴ 20
Thansk Herve', I will try. For reference this is the parallelization implementation of zellkonverter, to save anndata from SCE https://gi…
Comment: biomaRt rnorvegicus_gene_ensembl not available anymore
by
Jason
• 0
Any update on the resolution to this? I'm having the same issue with another species.
Votes
A: Recommendations for combining multiple 10x runs into one SingleCellExperiment
Answer: Handling biological replicates in DESeq2
Comment: biomaRt rnorvegicus_gene_ensembl not available anymore
biomaRt rnorvegicus_gene_ensembl not available anymore
A: Does edgeR need to specify reference group?
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