11
votes
1
answer
14k
views
1
answer
RPKM, CPM and TMM
rnaseq edger differential expression written 3.2 years ago by Pauly Lin80 • updated 3.2 years ago by Aaron Lun21k
20
votes
2
answers
9.7k
views
5 follow
2
answers
3
votes
2
answers
8.7k
views
2
answers
how to calculate gene length to be used in rpkm() in edgeR
rnaseq edger rpkm written 4.4 years ago by shirley zhang1.0k • updated 3.9 years ago by Gordon Smyth35k
10
votes
3
answers
8.6k
views
7 follow
3
answers
Batch correction in DESeq2
rnaseq deseq2 combat removebatcheffect() batch effect written 2.8 years ago by AB10 • updated 2.3 years ago by adam0
7
votes
3
answers
8.4k
views
3
answers
2
votes
2
answers
6.8k
views
5 follow
2
answers
Integrating DESeq2 and TopGO for Enrichment
rnaseq go deseq2 R written 3.6 years ago by nw32810 • updated 3.6 years ago by Bernd Klaus490
0
votes
1
answer
6.5k
views
1
answer
3D PCA Plot of RNA-seq Data using plotPCA from within DESeq2
rnaseq deseq2 pca written 3.5 years ago by erin.gill8130 • updated 3.5 years ago by Michael Love19k
12
votes
2
answers
6.0k
views
5 follow
2
answers
gene dispersion, what does it mean?
rnaseq gener written 2.8 years ago by tonja.r40 • updated 2.8 years ago by Gordon Smyth35k
3
votes
1
answer
5.7k
views
1
answer
Deseq2: RNA-seq and Negative binomial distribution
rnaseq deseq2 written 2.9 years ago by tony_cybercloud0 • updated 2.9 years ago by Michael Love19k
1
vote
1
answer
5.4k
views
1
answer
Undertanding how DESeq2 handles multiple test conditions
rnaseq deseq2 R written 3.6 years ago by nw32810 • updated 3.6 years ago by Ryan C. Thompson6.8k
3
votes
1
answer
5.3k
views
1
answer
DEseq2 - Use normalized DEseq2 counts to plot most expressed genes per group
rnaseq deseq2 R written 2.7 years ago by Bstn1320 • updated 2.7 years ago by Michael Love19k
4
votes
2
answers
5.1k
views
2
answers
2
votes
2
answers
5.1k
views
2
answers
12
votes
2
answers
4.9k
views
2
answers
How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
rnaseq annotationdbi written 24 months ago by gokce.ouz30 • updated 23 months ago by Valerie Obenchain ♦♦ 6.6k
5
votes
1
answer
4.5k
views
5 follow
1
answer
Ballgown vs (voom,edgeR,DESeq,limma)
rnaseq limma differential expression voom written 3.7 years ago by Fran├žois Lefebvre50 • updated 3.7 years ago by Alyssa Frazee200
2
votes
1
answer
4.4k
views
1
answer
Estimation of dispersion in DeSeq and DeSeq2
rnaseq deseq deseq2 written 3.8 years ago by JK10 • updated 3.8 years ago by Michael Love19k
3
votes
2
answers
4.3k
views
2
answers
Remove batch effect in small RNASeq study (SVA or others?)
rnaseq alignment edger sva written 4.4 years ago by shirley zhang1.0k • updated 3.7 years ago by Gordon Smyth35k
1
vote
1
answer
4.3k
views
1
answer
Deseq2 for RNAseq experiments without replicates
rnaseq deseq2 written 2.6 years ago by prp2910 • updated 2.6 years ago by Michael Love19k
3
votes
2
answers
4.1k
views
2
answers
limma voom accessing normalised counts tables
geneexpression rnaseq limma voom counts written 3.9 years ago by Peter Crisp10 • updated 3.9 years ago by Steve Lianoglou12k
19
votes
2
answers
3.9k
views
7 follow
2
answers
Usability of ERCC spike-ins in standard RNAseq experiments
rnaseq deseq2 ercc written 23 months ago by mbeckste20 • updated 23 months ago by Simon Anders3.5k
1
vote
1
answer
3.8k
views
1
answer
18
votes
2
answers
3.6k
views
6 follow
2
answers
9
votes
2
answers
3.4k
views
5 follow
2
answers
What to use: PCA or tSNE dimension reduction in DESeq2 analysis?
rnaseq deseq2 pca tsne written 14 months ago by s.w.vanderlaan20 • updated 14 months ago by Kushal K Dey10
7
votes
2
answers
3.4k
views
2
answers
9
votes
2
answers
3.2k
views
2
answers
Estimating and removing batch effects from rna-seq dataset
rnaseq limma sva removebatcheffect() batch effect written 2.9 years ago by AB10 • updated 2.9 years ago by Jeff Leek520
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