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Optimal edgeR design for a single-factor experiment
factors
edgeR
setup
DGELIst
updated 12 months ago by
Gordon Smyth
45k • written 12 months ago by
Alex
• 0
0
votes
2
replies
766
views
create DGElist Object
edger
DGElist
updated 3.1 years ago by
Gordon Smyth
45k • written 3.1 years ago by
naser.sadri
• 0
0
votes
4
replies
1.1k
views
Error in RnaSeqGeneEdgeRQL
dgelist
edger
RnaSeqGeneEdgeRQL
updated 3.8 years ago by
Gordon Smyth
45k • written 3.8 years ago by
Kevin
• 0
1
vote
4
replies
949
views
edgeR/DGEList add assays to a DGEList like in SummarizedExperiment
edgeR
summarizedexperiment
dgelist
4.1 years ago
aljoscha.leusmann
• 0
0
votes
0
replies
472
views
Using log2FC distance matrix in Boot.Phylo to create bootstrapped trees
tree
bootstrap
dgelist
plotmds
4.2 years ago
Larry K.
• 0
0
votes
1
reply
1.2k
views
DGEList remove/exclude rows with entrezgene = 'NA'
edger
dgelist
NA
egsea
updated 4.2 years ago by
Gordon Smyth
45k • written 4.2 years ago by
belmore
• 0
3
votes
3
replies
2.4k
views
Correct annotation of DGEList object from edgeR package regarding an RNA-Seq dataset
edger
DGEList
org.hs.eg.db
gene annotation
updated 7 months ago by
IIart.hubII
• 0 • written 4.5 years ago by
svlachavas
▴ 780
0
votes
2
replies
1.8k
views
Design of 'group' object in DGElist function
egder
dgelist
group
rnaseq
updated 4.5 years ago by
Aaron Lun
★ 27k • written 4.5 years ago by
fawazfebin
▴ 30
2
votes
4
replies
1.7k
views
Filtering DGEList object in edgeR
DGElist
filter
edgeR
updated 4.9 years ago by
Gordon Smyth
45k • written 4.9 years ago by
alakatos
▴ 120
2
votes
6
replies
1.4k
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 5.8 years ago by
Steve Lianoglou
13k • written 5.8 years ago by
benedict.ng
▴ 10
3
votes
7
replies
4.6k
views
edgeR subsetting DGEList by column/sample
edger
subsetting
dgelist
updated 5.8 years ago by
Gordon Smyth
45k • written 5.8 years ago by
mnaymik
▴ 10
1
vote
4
replies
16k
views
edgeR: non-unique values when setting 'row.names' - but the row names are unique!!!
edgeR
row.names
DGEList
7.3 years ago
ccheung
• 0
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Comment: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
by
James W. MacDonald
59k
We have progressed past the point where I show you how to do things using Bioconductor packages, and into the realm where I start telling y…
Comment: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
by
Yang Shi
• 0
Thanks sir! As your mentioned here, 12-15 means cutoff value about 4? Could I select the reflection point as the "point" that starts to ha…
Comment: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
by
James W. MacDonald
59k
It's a non-scientific selection. The Nonspecific probes are meant to be sequences that are not found in nature, so any binding is due to cr…
Comment: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
by
Yang Shi
• 0
Thanks for your excellent reply sir! But there are still some points confused me. (1).dbGetQuery get 93 kinds of probes. Would be okay for …
Comment: Print EnhancedVolcano Plot as jpeg or similar in R Notebook
by
Kevin Blighe
3.5k
Great! problem solved, then?
Votes
Answer: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
Answer: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
Comment: Quantile Normalization after rma or not?
Comment: Print EnhancedVolcano Plot as jpeg or similar in R Notebook
Comment: How to best visualize multi-level transcriptomics experiment data?
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