Showing : edger • reset
2
votes
4
replies
3.3k
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
2.1 years ago Sabiha ▴ 20
0
votes
3
replies
1.4k
views
EdgeR for methylation analysis when there is no replicates
RRBSdata edgeR
updated 2.1 years ago by 53k • written 2.1 years ago by • 0
3
votes
3
replies
2.2k
views
EdgeR: Should I include all samples/conditions in my dispersion estimation while only testing for certain contrasts
edgeR
updated 2.1 years ago by 53k • written 2.1 years ago by • 0
4
votes
9
replies
2.8k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2 edgeR
2.2 years ago • updated 2.1 years ago Luca • 0
0
votes
1
reply
655
views
download problem
edgeR
updated 2.2 years ago by 53k • written 2.2 years ago by • 0
0
votes
5
replies
1.5k
views
Help with model for differential expression analysis
DifferentialExpression edgeR
2.2 years ago • updated 2.1 years ago Lucy ▴ 60
1
vote
2
replies
1.5k
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
2.2 years ago Sabiha ▴ 20
5
votes
2
replies
1.8k
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 2.2 years ago by 53k • written 2.2 years ago by • 0
1
vote
2
replies
1.6k
views
EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 2.3 years ago by 53k • written 2.3 years ago by • 0
12
votes
5
replies
5.7k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 9 months ago by • 0 • written 2.3 years ago by • 0
0
votes
3
replies
1.5k
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
2.3 years ago Karthik • 0
6
votes
2
replies
2.5k
views
DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 2.3 years ago by 53k • written 2.3 years ago by ▴ 10
6
votes
7
replies
1.9k
views
[Bug] Segfault in edgeR::cpm
edgeR segfault
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by ▴ 20
0
votes
0
replies
800
views
Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
2.4 years ago Florian • 0
1
vote
3
replies
968
views
edgeR: Time course RNA-seq experiments
edgeR
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
0
votes
1
reply
919
views
Batch effect adjust in model matrix
BatchEffect edgeR
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
1
vote
6
replies
3.9k
views
Can I use EdgeR log2(cpm) instead of voom log2(cpm) to be analyzed as microarray data?
limma edger timecourse without replicate voom
written 9.3 years ago by ▴ 10
1
vote
4
replies
1.4k
views
MDS plot edgeR
edgeR
updated 2.5 years ago by 53k • written 2.5 years ago by ▴ 10
3
votes
3
replies
1.1k
views
comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression edgeR limma
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
1
vote
2
replies
2.2k
views
Should I use CPM or Voom transformed values for downstream analysis?
edgeR limma
2.5 years ago petertam1343 • 0
1
vote
5
replies
1.4k
views
Why do I obtain Identical Adj.P value when running edgeR ?
edgeR
updated 2.5 years ago by 53k • written 2.5 years ago by ▴ 30
3
votes
3
replies
1.2k
views
EdgeR and DESeq2, variance estimation and parametric test
parametrictest edgeR DESeq2
2.5 years ago Nisha • 0
2
votes
3
replies
1.7k
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 2.5 years ago by • 0
1
vote
5
replies
1.4k
views
edgeR design/contrast matrix troubles
edgeR
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
0
votes
1
reply
883
views
Is it possible to combine count gene expression data coming from one sequencing technology (RNA seq) with intensity gene expression data coming from …
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by • 0
2
votes
4
replies
2.2k
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 2.5 years ago by 43k • written 2.5 years ago by ▴ 10
0
votes
0
replies
2.3k
views
Tutorial: Read data file containing both counts and annotation into edgeR
rpkm edgeR featureCounts
2.5 years ago Gordon Smyth 53k
2
votes
7
replies
5.8k
views
EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 2.5 years ago by • 0 • written 4.9 years ago by ▴ 20
0
votes
8
replies
4.0k
views
Question about filterByExpr function edgeR
edgeR
2.5 years ago lucap • 0
0
votes
2
replies
801
views
EdgeR FTest
edgeR
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
2
votes
5
replies
2.0k
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
2.6 years ago duez.tolga • 0
0
votes
2
replies
1.4k
views
EdgeR and repeated measures: how to design a correct matrix having three time points
repeatedmeasure edgeR
2.6 years ago greta • 0
1
vote
1
reply
707
views
A query about selecting the coefficient in glmLRT to test for by index
edgeR
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
0
votes
9
replies
1.5k
views
estimateDisp() error
edgeR
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
4
votes
3
replies
1.9k
views
Custom design for scRNA DGE with pseudobulking
scRNAseq scrna paireddesign edgeR pseudobulking
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
4
votes
9
replies
4.7k
views
RNA seq differential expression analysis for large sample size
edgeR DESeq2
2.6 years ago Luca • 0
2
votes
5
replies
2.2k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R edgeR RNASeq
2.6 years ago mohammedtoufiq91 ▴ 10
6
votes
2
replies
1.4k
views
How to access the C++ code of the function .cxx_ave_log_cpm in the aveLogCPM.default function of EdgeR package?
edgeR
2.6 years ago Josué ▴ 20
1
vote
1
reply
1.0k
views
NA p values in edgeR results
DifferentialExpression edgeR
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
1
vote
2
replies
1.2k
views
edgeR, RRBS Library size preparation
RRBSdata edgeR methylationArrayAnalysis
2.7 years ago Krzysztof • 0
1
vote
1
reply
883
views
Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
3
votes
2
replies
1.3k
views
Does this RNAseq experiment require a repeated measures approach?
StatisticalMethod RNASeqData edgeR DESeq2
updated 2.7 years ago by 53k • written 2.7 years ago by ▴ 30
0
votes
5
replies
1.5k
views
Model and Contrasts with 4 variables
contrast edgeR DESeq2
updated 2.7 years ago by 68k • written 2.7 years ago by • 0
3
votes
6
replies
1.7k
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 2.8 years ago by 53k • written 2.8 years ago by ▴ 10
2
votes
1
reply
955
views
DESeq2 or edgeR for Presence and Absence of Proteins
edgeR DESeq2
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by • 0
5
votes
11
replies
8.5k
views
Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 2.8 years ago by ▴ 20
5
votes
7
replies
2.6k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 2.8 years ago by 53k • written 2.8 years ago by ▴ 10
0
votes
1
reply
1.0k
views
DESeq2 about comparasion of gene expression change on two-time points between two group samples.
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 2.8 years ago by ★ 1.4k • written 2.8 years ago by • 0
0
votes
1
reply
921
views
CI for logCPM (fitted values)
RNAseq edgeR
updated 2.8 years ago by 53k • written 2.8 years ago by ▴ 10
3
votes
4
replies
1.2k
views
Anova table edgeR limma
limma RNASeq edgeR
2.8 years ago KATHERINE CHUERE NUNES • 0
2,036 results • Page 3 of 41
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Answer: tximeta cannot open annotation gtf? by ATpoint ★ 5.0k
> Timeout of 60 seconds was reached You have to increase the default timeout limits for downloads, `options(timeout=3600)`. GENCODE serve…
Answer: GSEA error by James W. MacDonald 68k
At a very high level, the way non-model organisms are annotated is by using blast to find orthologs in other species that are well annotate…
Comment: Unable to find ENTREZ IDs by Adithi • 0
Hi James, Thank you so much for your reply. My main goal is to find ortholog genes from chinese hamster gene symbols to mouse gene symbols…
Comment: Unable to find ENTREZ IDs by Adithi • 0
Hi James, Thank you so much for your reply. My main goal is to find ortholog genes from chinese hamster gene symbols to mouse gene symbols…
Answer: Unable to find ENTREZ IDs by James W. MacDonald 68k
Those are the 'symbols', and are a concatenation of LOC and the NCBI Gene ID (what used to be called an Entrez Gene ID). As an example:http…
Votes
Answer: GSEA error
Answer: OrgDb for maize
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
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