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DGELIst
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0
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2
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449
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How to make DGEList and design matrix by edgeR package
DGEList
edgeR
10 months ago
prity6459
• 0
2
votes
2
replies
827
views
Inccorect group number in DGEList
edgeR
Bioconductor
Dseq2
dgelist
updated 2.2 years ago by
Gordon Smyth
52k • written 2.2 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 3.8 years ago by
Gordon Smyth
52k • written 3.8 years ago by
Alex
• 0
0
votes
2
replies
2.2k
views
create DGElist Object
edger
DGElist
updated 5.9 years ago by
Gordon Smyth
52k • written 5.9 years ago by
naser.sadri
• 0
0
votes
4
replies
2.0k
views
Error in RnaSeqGeneEdgeRQL
dgelist
edger
RnaSeqGeneEdgeRQL
updated 6.6 years ago by
Gordon Smyth
52k • written 6.6 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
6.8 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
6.9 years ago
Larry K.
• 0
0
votes
1
reply
2.5k
views
DGEList remove/exclude rows with entrezgene = 'NA'
edger
dgelist
NA
egsea
updated 7.0 years ago by
Gordon Smyth
52k • written 7.0 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 3.4 years ago by
IIart.hubII
• 0 • written 7.2 years ago by
svlachavas
▴ 840
0
votes
2
replies
3.6k
views
Design of 'group' object in DGElist function
egder
dgelist
group
rnaseq
updated 7.3 years ago by
Aaron Lun
★ 28k • written 7.3 years ago by
fawazfebin
▴ 60
2
votes
4
replies
3.7k
views
Filtering DGEList object in edgeR
DGElist
filter
edgeR
updated 7.6 years ago by
Gordon Smyth
52k • written 7.6 years ago by
alakatos
▴ 130
4
votes
6
replies
2.9k
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 8.5 years ago by
Steve Lianoglou
★ 13k • written 8.5 years ago by
benedict.ng
▴ 30
3
votes
7
replies
7.3k
views
edgeR subsetting DGEList by column/sample
edger
subsetting
dgelist
updated 8.6 years ago by
Gordon Smyth
52k • written 8.6 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
10.0 years ago
ccheung
• 0
14 results • Page
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Comment: How to formulate 2 factor nested design in DESeq2
by
Mariane
• 0
Hi JK Kim, I'm having a problem similar to the one you reported. Could you please tell me how you solved this problem? Thanks
Comment: batch effect removal for agilent microarray data
by
gaye.yilmaz
• 0
Thank you
Answer: Pathview visualisation not including positive log2 fold changes
by
James W. MacDonald
68k
Without providing a self-contained example, nobody can tell you if/where you went wrong. Since you get a KEGG pathway with some of the gene…
Comment: Differential variance analysis - can i use deseq2
by
Marwan
• 0
Thanks Michael for your answer, i didnt mean to use Deseq2 directly for the variance testing, but more like asking if using the (VST) data…
Answer: Differential variance analysis - can i use deseq2
by
Michael Love
43k
We don't have a test of differential variance but other Bioconductor packages can, check similar posts (even on the right side bar) or use …
Votes
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Suggesting changing the "reply-to" field to the mailing list address.
Answer: UniProt.ws query for single UniRef90 ID takes several minutes
A: How to extract DESeq2 results for an interaction design
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
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