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dgelist
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0
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2
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650
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How to make DGEList and design matrix by edgeR package
DGEList
edgeR
18 months ago • updated 17 months ago
prity6459
• 0
2
votes
2
replies
981
views
Inccorect group number in DGEList
edgeR
Bioconductor
Dseq2
dgelist
updated 2.8 years ago by
Gordon Smyth
53k • written 2.8 years ago by
Fiona
• 0
1
vote
1
reply
1.3k
views
Optimal edgeR design for a single-factor experiment
factors
edgeR
setup
DGELIst
updated 4.4 years ago by
Gordon Smyth
53k • written 4.4 years ago by
Alex
• 0
0
votes
2
replies
2.4k
views
create DGElist Object
edger
DGElist
updated 6.5 years ago by
Gordon Smyth
53k • written 6.5 years ago by
naser.sadri
• 0
0
votes
4
replies
2.2k
views
Error in RnaSeqGeneEdgeRQL
dgelist
edger
RnaSeqGeneEdgeRQL
updated 7.2 years ago by
Gordon Smyth
53k • written 7.2 years ago by
Kevin
• 0
1
vote
4
replies
2.9k
views
edgeR/DGEList add assays to a DGEList like in SummarizedExperiment
edgeR
summarizedexperiment
dgelist
7.5 years ago
aljoscha.leusmann
• 0
0
votes
0
replies
1.3k
views
Using log2FC distance matrix in Boot.Phylo to create bootstrapped trees
tree
bootstrap
dgelist
plotmds
7.6 years ago
Larry K.
• 0
0
votes
1
reply
2.7k
views
DGEList remove/exclude rows with entrezgene = 'NA'
edger
dgelist
NA
egsea
updated 7.6 years ago by
Gordon Smyth
53k • written 7.6 years ago by
belmore
• 0
3
votes
3
replies
4.4k
views
Correct annotation of DGEList object from edgeR package regarding an RNA-Seq dataset
edger
DGEList
org.hs.eg.db
gene annotation
updated 4.0 years ago by
IIart.hubII
• 0 • written 7.9 years ago by
svlachavas
▴ 840
0
votes
2
replies
3.8k
views
Design of 'group' object in DGElist function
egder
dgelist
group
rnaseq
updated 7.9 years ago by
Aaron Lun
★ 29k • written 7.9 years ago by
fawazfebin
▴ 60
2
votes
4
replies
4.1k
views
Filtering DGEList object in edgeR
DGElist
filter
edgeR
updated 8.3 years ago by
Gordon Smyth
53k • written 8.3 years ago by
alakatos
▴ 130
4
votes
6
replies
3.2k
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 9.2 years ago by
Steve Lianoglou
★ 13k • written 9.2 years ago by
benedict.ng
▴ 30
3
votes
7
replies
7.7k
views
edgeR subsetting DGEList by column/sample
edger
subsetting
dgelist
updated 9.2 years ago by
Gordon Smyth
53k • written 9.2 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
10.7 years ago
ccheung
• 0
14 results • Page
1 of 1
Recent ...
Replies
Comment: Help with defining groups
by
Phinney, Brett
▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness
by
massimo
• 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package
by
ksankaran
• 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
by
ATpoint
★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes
by
ATpoint
★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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