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10
votes
1
answer
1.5k
views
5 follow
1
answer
Bootstrap confidence intervals on RNA-seq expression from Kallisto
rnaseq limma edger deseq2 voom written 2.3 years ago by Sean Davis ♦ 20k • updated 22 hours ago by Paul Harrison • 60
0
votes
0
answers
32
views
0
answers
Differential expression of nomalised and log2 transformed data in limma
limma differential gene expression lmfit model.matrix written 1 day ago by stinehedensted • 0
0
votes
1
answer
55
views
1
answer
limma: Camera() about the input data
limma camera written 2 days ago by django_w • 0 • updated 1 day ago by Gordon Smyth ♦ 31k
1
vote
1
answer
69
views
1
answer
TREAT function - how to interpret the result
limma treat written 5 days ago by Sanches • 0 • updated 3 days ago by Gordon Smyth ♦ 31k
0
votes
2
answers
147
views
2
answers
Choosing genes for clustering
clustering limma differential gene expression feature selection hierarchical clustering written 10 days ago by lirongrossmann • 0 • updated 5 days ago by Gordon Smyth ♦ 31k
1
vote
0
answers
108
views
0
answers
Selecting genes that best separate between two groups
clustering genefilter limma tpm ttest written 5 days ago by lirongrossmann • 0
8
votes
1
answer
97
views
1
answer
Why edgeR::aveLogCPM() is simlar to log2(rowMeans(cpm)) instead of rowMeans(cpm(y, log=TRUE))
rnaseq limma edger independent filtering written 8 days ago by Robert Castelo • 2.0k
0
votes
1
answer
127
views
1
answer
Limma RNAseq comparison with Cuffdiff
limma written 10 days ago by Biorunner88 • 10 • updated 10 days ago by Gordon Smyth ♦ 31k
13
votes
4
answers
2.9k
views
7 follow
4
answers
Removing continuous covariate effects in limma analysis
microarray limma written 2.5 years ago by Pauly Lin • 50 • updated 11 days ago by Gordon Smyth ♦ 31k
7
votes
2
answers
195
views
2
answers
Limma and batch effect
clustering limma differential gene expression removebatcheffect written 11 days ago by lirongrossmann • 0 • updated 11 days ago by Gordon Smyth ♦ 31k
0
votes
1
answer
1.8k
views
1
answer
removeBatchEffect options: design and covariates
limma removebatcheffect written 3.1 years ago by Rao,Xiayu • 530 • updated 11 days ago by Gordon Smyth ♦ 31k
3
votes
2
answers
128
views
2
answers
Limma Singlet Moderated T-Test
limma written 11 weeks ago by andrew.j.skelton73 • 290 • updated 11 days ago by Gordon Smyth ♦ 31k
1
vote
1
answer
162
views
1
answer
Limma for differential expression in a time-course
limma differential expression multiple time points time-course written 12 days ago by Jake • 0 • updated 12 days ago by Aaron Lun • 16k
0
votes
0
answers
357
views
0
answers
Tximport with paired and single ended reads
limma bioconductor rna-seq written 5 weeks ago by chris86 • 320
0
votes
0
answers
146
views
0
answers
limma model including duplicated probes
limma written 15 days ago by kgorczak • 10
2
votes
1
answer
60
views
1
answer
No gene hits in cameraPR - due to bug dropping statistic names?
limma camera written 15 days ago by sarah.williams1 • 20 • updated 15 days ago by Gordon Smyth ♦ 31k
1
vote
1
answer
176
views
1
answer
Limma paired sample analysis
limma limma design matrix limma paired analysis written 16 days ago by anandprem1792 • 0
0
votes
0
answers
175
views
0
answers
how to build gene.pathway data.frame for non-model organism
limma topgo edger kegg dataframe written 16 days ago by mictadlo • 0
0
votes
1
answer
193
views
1
answer
How to use topGO and KEGG with de-novo species
limma topgo edger kegg kegga written 16 days ago by mictadlo • 0 • updated 16 days ago by Gordon Smyth ♦ 31k
0
votes
0
answers
48
views
0
answers
limma results more probes for same gene
limma written 17 days ago by Giovanni Calice • 150
2
votes
1
answer
366
views
1
answer
Why does limma contrast.fit produces NA's for all contrast although missing data only in one condition?
limma contrast lmfit missing data makecontrasts written 4 weeks ago by wewolski • 10 • updated 18 days ago by Gordon Smyth ♦ 31k
2
votes
1
answer
251
views
1
answer
plotMDS axis labels for limma/EdgeR: PCA or PCoA
limma edger written 19 days ago by andrew.lonsdale • 0 • updated 19 days ago by Gordon Smyth ♦ 31k
0
votes
2
answers
216
views
2
answers
A puzzle about the results of differential genes
limma written 20 days ago by llkxiaolan • 0
2
votes
2
answers
244
views
2
answers
Some questions about gene annotation
limma written 22 days ago by llkxiaolan • 0
0
votes
0
answers
237
views
0
answers
limma voom for single factor
limma differential expression voom written 22 days ago by bumbum • 0 • updated 22 days ago by Gordon Smyth ♦ 31k
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