Showing : edger • reset
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
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
3
votes
4
replies
8.5k
views
Gene-gene correlation analysis with RNA-seq
edgeR
updated 11 weeks ago by • 0 • written 10.8 years ago by ▴ 30
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 5 days ago by • 0 • written 8.8 years ago by ▴ 30
9
votes
5
replies
5.0k
views
Differential expression analysis: Permutation Test
deseq2 limma edger permutation
updated 4 months ago by 50k • written 8.2 years ago by ▴ 90
4
votes
12
replies
3.7k
views
Using edgeR and a spike-in to calculate absolute abundance
edgeR SpikeIn RNASeq
updated 6 months ago by • 0 • written 3.2 years ago by • 0
5
votes
11
replies
2.9k
views
Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 11 months ago by ▴ 20
2
votes
7
replies
2.9k
views
EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 7 months ago by • 0 • written 3.0 years ago by ▴ 20
0
votes
11
replies
2.7k
views
edgeR contrasts
edgeR
updated 8 months ago by 65k • written 19 months ago by • 0
1
vote
6
replies
2.6k
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 7.4 years ago by ▴ 10
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
2
votes
8
replies
2.2k
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
2
replies
2.0k
views
humann2 output appropriate for EdgeR or DESeq2 analysis
edger deseq2
updated 8 months ago by • 0 • written 6.3 years ago by • 0
0
votes
5
replies
1.8k
views
EdgeR: paired samples together with independant samples
RNASeq edgeR RNASeq edgeR
updated 22 days ago by 50k • written 11.5 years ago by ▴ 30
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 ★ 4.0k
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 3 months ago by 50k • written 3.0 years ago by ▴ 60
6
votes
10
replies
1.5k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 4 days ago by • 0 • written 14 months ago by ▴ 10
0
votes
1
reply
1.4k
views
EdgeR norm.factor input
Normalization edgeR Normalization edgeR
updated 4 months ago by 50k • written 10.2 years ago by ★ 13k
2
votes
5
replies
1.3k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 14 months ago by • 0
2
votes
5
replies
1.3k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R edgeR RNASeq
9 months ago mohammedtoufiq91 ▴ 10
0
votes
8
replies
1.3k
views
Question about filterByExpr function edgeR
edgeR
8 months ago lucap • 0
0
votes
3
replies
1.2k
views
EdgeR glm based analysis
edgeR edgeR
10.3 years ago • updated 8 months ago Gordon Smyth 50k
4
votes
9
replies
1.2k
views
RNA seq differential expression analysis for large sample size
edgeR DESeq2
9 months ago Luca • 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
4
votes
9
replies
1.1k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2 edgeR
3 months ago Luca • 0
0
votes
2
replies
1.1k
views
library size and fold changes
edgeR edgeR
updated 24 days ago by 50k • written 12.4 years ago by ▴ 670
4
votes
3
replies
1.0k
views
Custom design for scRNA DGE with pseudobulking
scRNAseq scrna paireddesign edgeR pseudobulking
updated 8 months ago by 50k • written 8 months ago by • 0
0
votes
0
replies
917
views
Tutorial: Read data file containing both counts and annotation into edgeR
rpkm edgeR featureCounts
7 months ago Gordon Smyth 50k
6
votes
7
replies
915
views
[Bug] Segfault in edgeR::cpm
edgeR segfault
updated 6 months ago by ★ 4.0k • written 6 months ago by ▴ 20
0
votes
4
replies
846
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 7 months ago by 41k • written 8 months ago by • 0
0
votes
9
replies
837
views
estimateDisp() error
edgeR
updated 8 months ago by 50k • written 8 months ago by • 0
1
vote
5
replies
833
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
8 months ago duez.tolga • 0
3
votes
6
replies
825
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 10 months ago by 50k • written 10 months ago by ▴ 10
2
votes
3
replies
793
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 8 months ago by • 0
0
votes
3
replies
791
views
edgeR DEGs multilevel
edgeR RNASeq DifferentialRegulation
updated 12 months ago by 50k • written 12 months ago by • 0
1
vote
3
replies
780
views
Is it okay to increase filtering to get more significant Adjusted P Values for DEGs found using Limma?
RNASeqPower edgeR DifferentialExpression limma RNASeq
updated 11 months ago by 50k • written 11 months ago by • 0
0
votes
5
replies
773
views
Model and Contrasts with 4 variables
contrast edgeR DESeq2
updated 10 months ago by 65k • written 10 months ago by • 0
1
vote
2
replies
756
views
Should I use CPM or Voom transformed values for downstream analysis?
edgeR limma
7 months ago petertam1343 • 0
7
votes
2
replies
754
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 4 months ago by 50k • written 4 months ago by • 0
1
vote
5
replies
719
views
Why do I obtain Identical Adj.P value when running edgeR ?
edgeR
updated 7 months ago by 50k • written 7 months ago by ▴ 30
1
vote
4
replies
707
views
MDS plot edgeR
edgeR
updated 7 months ago by 50k • written 7 months ago by ▴ 10
6
votes
2
replies
698
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
3
votes
4
replies
698
views
Anova table edgeR limma
limma RNASeq edgeR
11 months ago KATHERINE CHUERE NUNES • 0
0
votes
11
replies
694
views
Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 7 weeks ago by 50k • written 8 weeks ago by • 0
5
votes
3
replies
681
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 27 days ago by 50k • written 4 weeks ago by ▴ 50
3
votes
2
replies
661
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
1
vote
5
replies
656
views
edgeR design/contrast matrix troubles
edgeR
updated 7 months ago by 65k • written 7 months ago by • 0
0
votes
2
replies
655
views
EdgeR and repeated measures: how to design a correct matrix having three time points
repeatedmeasure edgeR
8 months ago greta • 0
3
votes
3
replies
644
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
2
votes
1
reply
633
views
edgeR with Successive Differences Contrast Coding?
hypothesisTesting contrastCoding edger ExperimentalDesign expressionDifferences
updated 12 months ago by 50k • written 12 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: How to retrieve gene ontology GO class? by bandconductor • 0
Sorry I wasn't clear before. What I mean is the all the information associated with the go term, such as description and evidence. I have …
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
How am i making the data? I am using the DESeq2 output data which I had generated
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq by Michael Love 41k
Sounds reasonable. For ranking genes, you could choose those with low decay rate but removing thoses where it is indistinguishable from …
Answer: Citation for edgeR user guide by Gordon Smyth 50k
Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You are just making up data? What is the point of this exercise?
Votes
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
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