Showing : edger • reset
3
votes
6
replies
82
views
LogFC values in edgeR - w/wo intercept
design.matrix logFC intercept edgeR model.matrix
7 hours ago • updated 3 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 45k • written 2 days ago by ▴ 10
0
votes
1
reply
60
views
after calcNormFactors with EdgeR, how to get TMM normalized matrix?
Normalization edgeR
updated 6 days ago by 45k • written 7 days ago by • 0
3
votes
3
replies
119
views
edgeR: the F-statistics changed after removing lowly expressed gene
glmQLFTest edgeR
updated 7 days ago by 45k • written 8 days ago by • 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 45k • written 13 days ago by • 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 45k • written 14 days ago by • 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 45k • written 22 days ago by • 0
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 45k • written 26 days ago by • 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 45k • written 4 weeks ago by • 0
0
votes
4
replies
265
views
Extremely different results for both EdgeR and DESeq2 analysis
edgeR DESeq2
updated 29 days ago by 45k • written 4 weeks ago by • 0
2
votes
5
replies
260
views
edgeR: Combining time series analysis with mock and treated samples
edgeR
4 weeks ago venura • 0
0
votes
2
replies
110
views
edgeR
rnaseq edgeR
updated 5 weeks ago by 45k • written 5 weeks ago by • 0
0
votes
11
replies
320
views
Differential methilation analysis - Design matrix not of full rank
DifferentialMethylation RRBSdata edgeR
updated 14 days ago by 45k • written 5 weeks ago by • 0
5
votes
6
replies
257
views
Large difference in PCA plot based on LCPM (log counts per million) and VST (variance stabilizing transformations)
PCAtools edgeR pcaExplorer RNASeq RNAseq123
5 weeks ago Alan • 0
0
votes
1
reply
95
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 5 weeks ago by 45k • written 5 weeks ago by • 0
2
votes
4
replies
190
views
I want to clarify difference between below two codes for analysis of DEGs. I got two different answers with these two methods and would like to know …
edgeR
6 weeks ago devi • 0
0
votes
1
reply
92
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 6 weeks ago by 37k • written 6 weeks ago by • 0
0
votes
2
replies
331
views
RNA-seq: problems with edgeR installation
BiocManager edgeR
updated 6 weeks ago by ★ 1.2k • written 7 weeks ago by • 0
0
votes
0
replies
90
views
edgeR testing interactions between two factors while controlling for blocking factor
edgeR ExpressionData RNASeqData
7 weeks ago Mafalda • 0
0
votes
1
reply
170
views
Why does my volcano plot look weird?
edgeR volcano_plot
updated 8 weeks ago by 45k • written 8 weeks ago by • 0
2
votes
17
replies
638
views
How to reduce the impact of one varaible in Deseq2 or edgeR for multivariate value analysis?
MultipleComparison edgeR DESeq2
written 8 weeks ago by • 0
0
votes
0
replies
98
views
Create a Gene Enrichment GO plot from goana output
goana RNASeq edgeR RnaSeq GO
8 weeks ago Raito92 ▴ 60
2
votes
3
replies
227
views
Classic or GLM approach in edgeR, Why do I got less DEG in GLM approach?
edgeR DEGs
updated 8 weeks ago by 45k • written 8 weeks ago by • 0
15
votes
18
replies
502
views
Is goana function for Gene Ontology enrichement analysis suitable for both edgeR and DESeq2 DEGs lists?
DESeq2 edgeR goana GO
updated 8 weeks ago by 45k • written 9 weeks ago by ▴ 60
2
votes
1
reply
134
views
How to determine which model (GLM and QLF or classic edgeR) to use for DGE analysis?
edgeR
updated 9 weeks ago by 45k • written 9 weeks ago by • 0
6
votes
2
replies
167
views
The number of controls versus treatment in differential expression analysis
DESeq2 edgeR limma
updated 9 weeks ago by 45k • written 9 weeks ago by ▴ 30
0
votes
1
reply
135
views
Edge R Error in quantile.default(zresid, probs = prob) : missing values and NaN's not allowed if 'na.rm' is FALSE
diffSpliceDGE RNASeq DifferentialSplicingWorkflow AlternativeSplicing edgeR
updated 9 weeks ago by 45k • written 9 weeks ago by • 0
1
vote
2
replies
197
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 10 weeks ago by ★ 4.4k • written 10 weeks ago by • 0
0
votes
2
replies
150
views
Gene Onotology: Can't get the goana function to work
edgeR GO
11 weeks ago Adelyn • 0
2
votes
5
replies
271
views
DESeq2 with baseline correction for gene expression differences
DESeq2 edgeR Transcriptomics
updated 11 weeks ago by 37k • written 12 weeks ago by • 0
1
vote
1
reply
171
views
edgeR for SDE analysis
RNASeqRData edgeR RNASeqR RNASeqData
updated 3 months ago by 45k • written 3 months ago by • 0
0
votes
2
replies
224
views
Extend comparisons between two groups to more groups in DESEQ2
edgeR DEGs DESEQ2 RNASeqData
3 months ago Raito92 ▴ 60
0
votes
2
replies
205
views
filterbyexp() in edgeR
edgeR
updated 3 months ago by 45k • written 3 months ago by • 0
0
votes
6
replies
405
views
Performing simple pairwise comparisons in DESEQ2
edgeR DEG RNASeq DESEQ2
updated 3 months ago by 37k • written 3 months ago by ▴ 60
2
votes
3
replies
328
views
Differential gene expression and (adjusted) p-values
edgeR StatisticalMethod
updated 22 days ago by • 0 • written 3 months ago by • 0
0
votes
3
replies
413
views
using the goana function from edgeR
RNASeq edgeR GO GOSemSim
updated 3 months ago by 45k • written 4 months ago by ▴ 70
1
vote
4
replies
343
views
Differential Splicing using edgeR
diffSpliceDGE edgeR DifferentialSplicing
4 months ago • updated 3 months ago Assa Yeroslaviz ★ 1.5k
3
votes
6
replies
410
views
How to use subjunc for differential splicing analysis?
subjunc edgeR
4 months ago Assa Yeroslaviz ★ 1.5k
2
votes
2
replies
206
views
catchKallisto results are not counts
DifferentialSplicingWorkflow catchKallisto edgeR DifferentialSplicing
4 months ago Assa Yeroslaviz ★ 1.5k
0
votes
1
reply
208
views
First time Statistical Analysis of RNA-seq
edgeR RNA-Seq log2 foldchange q_value
updated 4 months ago by 45k • written 4 months ago by • 0
0
votes
5
replies
375
views
ANOVA-like vs direct contrast
edgeR
4 months ago fcamus • 0
2
votes
2
replies
989
views
EdgeR installation issue
limma edgeR DESeq2
4 months ago aonghus • 0
0
votes
2
replies
234
views
Filtering low coverage RRBS counts results in few reads. Any alternatives?
limma edgeR
updated 5 months ago by • 0 • written 5 months ago by • 0
3
votes
2
replies
340
views
Multi-level design RRBS analysis with voomLmFit
edgeR voomLmFit limma duplicateCorrelation voom
6 months ago altintas.ali • 0
50 results • Page 1 of 1
Recent ...
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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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