Showing : edgeR • reset
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 14 days ago by • 0 • written 8.8 years ago by ▴ 30
9
votes
5
replies
5.1k
views
Differential expression analysis: Permutation Test
deseq2 limma edger permutation
updated 5 months ago by 50k • written 8.2 years ago by ▴ 90
7
votes
2
replies
798
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 5 months ago by 50k • written 5 months ago by • 0
6
votes
2
replies
711
views
How to access the C++ code of the function .cxx_ave_log_cpm in the aveLogCPM.default function of EdgeR package?
edgeR
9 months ago Josué ▴ 20
6
votes
10
replies
1.6k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 13 days ago by • 0 • written 15 months ago by ▴ 10
6
votes
7
replies
943
views
[Bug] Segfault in edgeR::cpm
edgeR segfault
updated 6 months ago by ★ 4.1k • written 6 months ago by ▴ 20
6
votes
7
replies
564
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 3 months ago by 50k • written 3 months ago by • 0
5
votes
7
replies
10.0k
views
threshold to filter lowly expressed genes
edger rnaseq
updated 3 months ago by • 0 • written 7.1 years ago by • 0
5
votes
6
replies
417
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 20 days ago by ★ 4.1k • written 23 days ago by ▴ 30
5
votes
9
replies
2.5k
views
edgeR: Should there be a normalization step for CRISPR screens? How to deal with bottlenecked screens?
edger calcnormfactors
updated 8 months ago by • 0 • written 6.4 years ago by ▴ 10
5
votes
4
replies
388
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
10 weeks ago pl23 • 0
5
votes
7
replies
1.2k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 11 months ago by 50k • written 11 months ago by ▴ 10
5
votes
11
replies
3.0k
views
Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 11 months ago by ▴ 20
5
votes
2
replies
551
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 4 months ago by 50k • written 4 months ago by • 0
5
votes
3
replies
709
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 5 weeks ago by 50k • written 6 weeks ago by ▴ 50
4
votes
6
replies
406
views
FilterByExpr low counts with small sample size
edgeR
15 days ago • updated 10 days ago Jonathan ▴ 10
4
votes
3
replies
1.8k
views
catchSalmon for tx-level DE
catchSalmon edgeR
updated 5 months ago by 50k • written 3.5 years ago by ★ 4.1k
4
votes
9
replies
1.1k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2 edgeR
3 months ago Luca • 0
4
votes
4
replies
430
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 3 months ago by 65k • written 3 months ago by • 0
4
votes
2
replies
624
views
DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 6 months ago by 50k • written 6 months ago by ▴ 10
4
votes
3
replies
1.0k
views
Custom design for scRNA DGE with pseudobulking
scRNAseq scrna paireddesign edgeR pseudobulking
updated 9 months ago by 50k • written 9 months ago by • 0
4
votes
9
replies
1.3k
views
RNA seq differential expression analysis for large sample size
edgeR DESeq2
9 months ago Luca • 0
4
votes
12
replies
3.7k
views
Using edgeR and a spike-in to calculate absolute abundance
edgeR SpikeIn RNASeq
updated 7 months ago by • 0 • written 3.2 years ago by • 0
4
votes
7
replies
13k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq R edgeR
updated 7 months ago by 50k • written 22 months ago by ▴ 30
3
votes
1
reply
164
views
Log-cpm values from limma
limma edgeR RNASeq
updated 14 days ago by 50k • written 15 days ago by • 0
3
votes
3
replies
542
views
EdgeR and DESeq2, variance estimation and parametric test
parametrictest edgeR DESeq2
7 months ago Nisha • 0
3
votes
2
replies
672
views
Does this RNAseq experiment require a repeated measures approach?
StatisticalMethod RNASeqData edgeR DESeq2
updated 10 months ago by 50k • written 10 months ago by ▴ 10
3
votes
2
replies
419
views
How does one test for interactions in EdgeR?
edgeR
11 weeks ago pl23 • 0
3
votes
1
reply
1.7k
views
Is it always preferable to recount library sizes of DGEList object in edgeR after filtering?
edgeR RnaSeqSampleSizeData RNAseq
updated 4 months ago by 50k • written 3.0 years ago by ▴ 60
3
votes
6
replies
840
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 11 months ago by 50k • written 11 months ago by ▴ 10
3
votes
4
replies
8.6k
views
Gene-gene correlation analysis with RNA-seq
edgeR
updated 3 months ago by • 0 • written 10.8 years ago by ▴ 30
3
votes
3
replies
669
views
EdgeR: Should I include all samples/conditions in my dispersion estimation while only testing for certain contrasts
edgeR
updated 3 months ago by 50k • written 3 months ago by • 0
3
votes
3
replies
569
views
comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression edgeR limma
updated 7 months ago by 65k • written 7 months ago by • 0
3
votes
4
replies
422
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 8 weeks ago by 50k • written 8 weeks ago by ▴ 50
3
votes
5
replies
372
views
Differing results from plotMDS and PCAtools
edgeR PCAtools
updated 4 weeks ago by 50k • written 5 weeks ago by • 0
3
votes
4
replies
708
views
Anova table edgeR limma
limma RNASeq edgeR
11 months ago KATHERINE CHUERE NUNES • 0
3
votes
3
replies
325
views
permutation test in edgeR
rna-seq edgeR
updated 12 days ago by 50k • written 25 days ago by • 0
2
votes
6
replies
404
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
10 weeks ago tsl0026 • 0
2
votes
4
replies
582
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
3 months ago Sabiha ▴ 20
2
votes
1
reply
602
views
DESeq2 or edgeR for Presence and Absence of Proteins
edgeR DESeq2
updated 11 months ago by ★ 4.1k • written 11 months ago by • 0
2
votes
3
replies
291
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
2
votes
2
replies
259
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
7 weeks ago Sabiha ▴ 20
2
votes
3
replies
364
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 12 weeks ago by 65k • written 12 weeks ago by • 0
2
votes
2
replies
2.0k
views
humann2 output appropriate for EdgeR or DESeq2 analysis
edger deseq2
updated 8 months ago by • 0 • written 6.4 years ago by • 0
2
votes
3
replies
805
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 8 months ago by • 0
2
votes
5
replies
1.4k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 14 months ago by • 0
2
votes
7
replies
2.9k
views
EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 8 months ago by • 0 • written 3.0 years ago by ▴ 20
2
votes
8
replies
2.3k
views
Error in DGEList(counts = cnt, group = group) : non-numeric values found in counts
edgeR
12 months ago • updated 11 months ago Luis • 0
2
votes
5
replies
1.4k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R edgeR RNASeq
9 months ago mohammedtoufiq91 ▴ 10
2
votes
2
replies
256
views
between lane normalization upper quantile
EDASeq edgeR
7 weeks ago • updated 6 weeks ago elesofi • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Timecourse RNASeq analysis by Aurora • 0
I managed to run ImpulseDE2 as I am interested in getting significant gene changes over time. Now I would like to run deseq as well and com…
Comment: Once again a "Model matrix not full rank" by arfranco ▴ 130
But.. How to run a temporal assay?
Comment: Deseq2 and Normalization of RNA sequencing data by kcarey • 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP by Gordon Smyth 50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma by Gordon Smyth 50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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