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DGELIst
•
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0
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2
replies
475
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How to make DGEList and design matrix by edgeR package
DGEList
edgeR
11 months ago
prity6459
• 0
2
votes
2
replies
850
views
Inccorect group number in DGEList
edgeR
Bioconductor
Dseq2
dgelist
updated 2.3 years ago by
Gordon Smyth
52k • written 2.3 years ago by
Fiona
• 0
1
vote
1
reply
1.2k
views
Optimal edgeR design for a single-factor experiment
factors
edgeR
setup
DGELIst
updated 3.9 years ago by
Gordon Smyth
52k • written 3.9 years ago by
Alex
• 0
0
votes
2
replies
2.3k
views
create DGElist Object
edger
DGElist
updated 6.0 years ago by
Gordon Smyth
52k • written 6.0 years ago by
naser.sadri
• 0
0
votes
4
replies
2.0k
views
Error in RnaSeqGeneEdgeRQL
dgelist
edger
RnaSeqGeneEdgeRQL
updated 6.7 years ago by
Gordon Smyth
52k • written 6.7 years ago by
Kevin
• 0
1
vote
4
replies
2.6k
views
edgeR/DGEList add assays to a DGEList like in SummarizedExperiment
edgeR
summarizedexperiment
dgelist
7.0 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
7.0 years ago
Larry K.
• 0
0
votes
1
reply
2.6k
views
DGEList remove/exclude rows with entrezgene = 'NA'
edger
dgelist
NA
egsea
updated 7.1 years ago by
Gordon Smyth
52k • written 7.1 years ago by
belmore
• 0
3
votes
3
replies
4.2k
views
Correct annotation of DGEList object from edgeR package regarding an RNA-Seq dataset
edger
DGEList
org.hs.eg.db
gene annotation
updated 3.5 years ago by
IIart.hubII
• 0 • written 7.3 years ago by
svlachavas
▴ 840
0
votes
2
replies
3.6k
views
Design of 'group' object in DGElist function
egder
dgelist
group
rnaseq
updated 7.4 years ago by
Aaron Lun
★ 28k • written 7.4 years ago by
fawazfebin
▴ 60
2
votes
4
replies
3.8k
views
Filtering DGEList object in edgeR
DGElist
filter
edgeR
updated 7.7 years ago by
Gordon Smyth
52k • written 7.7 years ago by
alakatos
▴ 130
4
votes
6
replies
3.0k
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 8.6 years ago by
Steve Lianoglou
★ 13k • written 8.6 years ago by
benedict.ng
▴ 30
3
votes
7
replies
7.4k
views
edgeR subsetting DGEList by column/sample
edger
subsetting
dgelist
updated 8.7 years ago by
Gordon Smyth
52k • written 8.7 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
10.1 years ago
ccheung
• 0
14 results • Page
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Answer: DESeq2
by
ATpoint
★ 4.8k
Time courses are often inevitable batches but you should have done the library prep at the same day, just extract RNA per day. If not then …
Comment: Package developing and interoperation with Bioconductor
by
slizchap
• 0
Thank you so much for your answer. This was very useful, I will optimize my functions so they can handle SE objects.
Comment: Package developing and interoperation with Bioconductor
by
slizchap
• 0
Thank you so much for your answer, very useful!
Comment: Error in H5Dclose(h5dataset) when trying to read in kallisto h5 files
by
Mike Smith
★ 6.6k
Tricky to try and debug this without some example files to work with. Can you provide the output of `traceback()` called immediately after…
Answer: Mismatch between Illumina Mouse Methylation BeadChip annotation and genome brows
by
James W. MacDonald
68k
The annotation data that is provided for this array is simply a repackaging of data that we get from Illumina, so any apparent inconsistenc…
Votes
Is it possible to speed up VariantAnnotation's rowRanges function when converting to a dataframe?
Answer: Is it possible to speed up VariantAnnotation's rowRanges function when convertin
Comment: ComBat with repeated measures
Answer: Package developing and interoperation with Bioconductor
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2?
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