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LogFC values in edgeR - w/wo intercept
design.matrix
logFC
intercept
edgeR
model.matrix
8 hours ago • updated 4 hours ago
JK Kim
• 0
3
votes
3
replies
111
views
Question on RNA-Seq single sample data analysis in EdgeR
R
edgeR
limma
RNASeq
Normalization
updated 1 day ago by
Gordon Smyth
45k • written 2 days ago by
mohammedtoufiq91
▴ 10
5
votes
5
replies
2.4k
views
how to understand cpm=1 and how filterByExpr works?
edger
updated 7 days ago by
gowthamee
• 0 • written 20 months ago by
linouhao
▴ 20
0
votes
1
reply
60
views
after calcNormFactors with EdgeR, how to get TMM normalized matrix?
Normalization
edgeR
updated 6 days ago by
Gordon Smyth
45k • written 7 days ago by
kevin
• 0
3
votes
3
replies
119
views
edgeR: the F-statistics changed after removing lowly expressed gene
glmQLFTest
edgeR
updated 7 days ago by
Gordon Smyth
45k • written 8 days ago by
Pei
• 0
1
vote
1
reply
86
views
could edgeR be applied to gene counts by gene family to make group comparisons?
edgeR
updated 13 days ago by
Gordon Smyth
45k • written 13 days ago by
eliza_3176
• 0
2
votes
6
replies
175
views
Variance explained (coefficient of determination) in edgeR
edgeR
14 days ago • updated 8 days ago
Gemma
• 0
0
votes
1
reply
66
views
Locating nearest genes in RRBS analysis
hiAnnotator
bsseq
DifferentialMethylation
edgeR
RRBSdata
updated 14 days ago by
Gordon Smyth
45k • written 14 days ago by
Mageiros
• 0
2
votes
2
replies
118
views
edgeR: How to display/plot individual miRNAs found to be differentialy expressed?
miRNAData
miRNA
DifferentialExpression
edgeR
20 days ago • updated 19 days ago
Sarah
• 0
0
votes
2
replies
171
views
Variance explained (coefficient of determination) in glmFit / glmLRT
edgeR
21 days ago • updated 19 days ago
Gemma
• 0
0
votes
1
reply
102
views
How to directly decet the outlier samples (libraries) in EdgeR pipeline
edgeR
updated 22 days ago by
Gordon Smyth
45k • written 22 days ago by
Mohamed
• 0
5
votes
14
replies
2.7k
views
Possible ways to select differential expressed genes using DeSeq2 or edgeR
R
deseq2
edger
differential gene expression
fold change
updated 23 days ago by
ATpoint
★ 1.2k • written 3.9 years ago by
Beginner
▴ 50
0
votes
0
replies
59
views
diffcyt - topTable function returns one total significance estimate instead of one per comparison
limma
diffcyt
edgeR
25 days ago
stefanos.bamopoulos
• 0
1
vote
1
reply
95
views
Should I keep libsizes?
Normalization
edgeR
updated 26 days ago by
Gordon Smyth
45k • written 26 days ago by
Barista
• 0
2
votes
7
replies
232
views
edgeR: topTags weird behavior - outputting NAs
edgeR
27 days ago • updated 23 days ago
venura
• 0
0
votes
2
replies
108
views
edgeR: Analyzing multiple factors with batch effects
edgeR
29 days ago
venura
• 0
0
votes
11
replies
422
views
EdgeR function nearestTSS() fails with org.Ss.eg.db
Sus_scrofa
edgeR
updated 28 days ago by
Gordon Smyth
45k • written 4 weeks ago by
Jon
• 0
0
votes
4
replies
266
views
Extremely different results for both EdgeR and DESeq2 analysis
edgeR
DESeq2
updated 29 days ago by
Gordon Smyth
45k • written 4 weeks ago by
melatoninixo
• 0
0
votes
11
replies
320
views
Differential methilation analysis - Design matrix not of full rank
DifferentialMethylation
RRBSdata
edgeR
updated 14 days ago by
Gordon Smyth
45k • written 5 weeks ago by
Mageiros
• 0
2
votes
3
replies
328
views
Differential gene expression and (adjusted) p-values
edgeR
StatisticalMethod
updated 22 days ago by
ruez.richard
• 0 • written 3 months ago by
tmms
• 0
7
votes
12
replies
2.7k
views
.fastq to .txt conversion for EdgeR package and merging two paired end sequence files
EdgeR
normalization
fastq
txt
TMM
updated 15 days ago by
Gordon Smyth
45k • written 6.5 years ago by
hamidrezarazzaghian
• 0
2
votes
6
replies
811
views
removing genes before RNA-seq normalization
edger
deseq2
normalization
removing genes
updated 29 days ago by
Gordon Smyth
45k • written 2.5 years ago by
aec
▴ 90
3
votes
3
replies
5.1k
views
TPM data Differential expression analysis
edger
limma
differential gene expression
updated 7 days ago by
Gordon Smyth
45k • written 4.1 years ago by
ghmdsr
• 0
5
votes
3
replies
2.7k
views
edgeR - how to convert DGELRT and other classes to .csv files
edgeR
differential expression
file conversion
updated 1 day ago by
Benjamin
• 0 • written 6.2 years ago by
cellbiologyhelp
▴ 10
1
vote
3
replies
3.9k
views
edgeR: what to do with no replicates
edgeR
10.5 years ago • updated 2 days ago
Gordon Smyth
45k
25 results • Page
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Comment: Error in h(simpleError(msg, call)) : when calling makeOrgPackagefromNCBI()
by
Lan Anh
• 0
Hello, Sorry for the late answer, I called several packages after my error and I do not know how it worked after that. Thank you for the h…
Comment: LogFC values in edgeR - w/wo intercept
by
JK Kim
• 0
Thanks, Dr. Smyth!
Comment: LogFC values in edgeR - w/wo intercept
by
JK Kim
• 0
Oops. I just corrected the URL. Thank you Dr. Smyth.
Comment: Fail to run RupRadar
by
Qingwei
• 0
Dear Sergi, Yeah, it works. ```r dm <- analyzeDuprates(bamDuprm,gtf,stranded,paired,threads, GTF.featureType="cDNA_match", GTF.attrType="ID…
Comment: LogFC values in edgeR - w/wo intercept
by
Gordon Smyth
45k
The link you've entered for "A guide to creating design matrices for gene expression experiments" doesn't work. Could you please correct th…
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Comment: LogFC values in edgeR - w/wo intercept
Answer: LogFC values in edgeR - w/wo intercept
Answer: LogFC values in edgeR - w/wo intercept
Answer: broken chain import in liftOver
Answer: toGRanges help!
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