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2
votes
1
answer
120
views
1
answer
extracting the genes associated with the groups or samples in pheatmap.
microarray R written 22 days ago by morteza.hadizade • 10 • updated 21 days ago by Malcolm Cook • 1.5k
7
votes
1
answer
132
views
1
answer
MultiAssayExperiment: Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
tcga multiassayexperiment wide format written 28 days ago by mario.zanfardino • 140 • updated 26 days ago by Marcel Ramos ♦♦ 310
3
votes
1
answer
50
views
1
answer
Limma without eBayes, is it indistunguishable from Ordinary Least Square?
bayesian limma ebayes ls written 12 days ago by CantExitVIM • 10 • updated 12 days ago by Gordon Smyth ♦ 35k
3
votes
1
answer
50
views
1
answer
converting a fasta file to .2bit format
biostrings rtracklayer written 12 days ago by saripalligautam86 • 10 • updated 12 days ago by Hervé Pagès ♦♦ 13k
4
votes
1
answer
46
views
1
answer
limma barcodeplot(): calculation of enrichment score
limma gene set enrichment analysis written 3 days ago by khandarius • 20 • updated 3 days ago by Aaron Lun • 21k
2
votes
2
answers
64
views
2
answers
Queries related to limma package based analysis of masspectrometry data
limma written 3 days ago by manubhaikp • 10 • updated 3 days ago by Gordon Smyth ♦ 35k
5
votes
1
answer
52
views
1
answer
How to set up appropriate analysis using sample type and condition for DESeq2
deseq2 design differential gene expression written 4 days ago by newbio17 • 0 • updated 3 days ago by Michael Love ♦ 19k
6
votes
1
answer
93
views
1
answer
How barcode-plot enrichment is calculated?
limma camera barcodeplot written 23 days ago by elim • 0 • updated 23 days ago by Gordon Smyth ♦ 35k
1
vote
0
answers
72
views
0
answers
News: Gene Ontology Official Workshop - Montreal, October 16, 2018
go gene ontology news bioinformatics genomics ontology written 23 days ago by laurent.albou • 0
1
vote
1
answer
66
views
1
answer
Visualise gene set analysis plot
limma gene set analysis gene set enrichment written 24 days ago by jaynishshah • 0 • updated 24 days ago by Gordon Smyth ♦ 35k
7
votes
2
answers
97
views
2
answers
Dispersion fit and p-value distributions
rnaseq deseq2 fdrtool written 3 days ago by C T • 90 • updated 2 days ago by Ryan C. Thompson ♦ 6.9k
3
votes
1
answer
85
views
1
answer
Differential analysis of multiple samples with different time points
diffbind R atac-seq written 7 days ago by firas • 0 • updated 5 days ago by Rory Stark • 2.6k
4
votes
1
answer
53
views
1
answer
no import.bam function in CAGEr version 1.22.3
cager written 13 days ago by Pengcheng Yang • 50
3
votes
1
answer
108
views
1
answer
use only lib size as normalizing factor in edgeR
edger written 4 weeks ago by Udi Landau • 30 • updated 29 days ago by Aaron Lun • 21k
2
votes
1
answer
111
views
1
answer
why the logFC is different between edgeR,DESeq2 results and fpkm logFC(log2(FPKM_tumor_mean/FPKM_normal_mean)?
edger deseq2 counts fpkm fc written 29 days ago by ZihaoXing • 0 • updated 28 days ago by Gordon Smyth ♦ 35k
5
votes
1
answer
108
views
1
answer
nestedF in decideTests: an analogue of Anova with post-hoc t-tests?
limma anova decidetests written 23 days ago by mikhael.manurung • 10 • updated 22 days ago by Gordon Smyth ♦ 35k
0
votes
0
answers
54
views
0
answers
Bookdown for bioC?
bookdown written 25 days ago by kimanh.lecao • 0
1
vote
0
answers
71
views
0
answers
No gene set have size > 10 ...
clusterprofiler gene ontology written 2 days ago by anton.kratz • 40
0
votes
0
answers
69
views
0
answers
Multiple alignment of big DNA sequences files
genome multiplealignment written 26 days ago by Giuseppe • 20
1
vote
1
answer
93
views
1
answer
DESeq2 for large de novo transcripts assembly
deseq2 written 6 days ago by Emiliano Canton • 10 • updated 6 days ago by Michael Love ♦ 19k
0
votes
2
answers
89
views
2
answers
Limma Volcano Plot Highlight Top Genes by Color
microarray limma volcanoplot color written 9 days ago by dmm204 • 0 • updated 9 days ago by Gordon Smyth ♦ 35k
3
votes
2
answers
136
views
2
answers
Batch correction when only some subjects have replicates across batches
limma rna-seq batch effect written 25 days ago by Mike A • 10 • updated 24 days ago by Peter Langfelder • 1.6k
0
votes
1
answer
74
views
1
answer
Bioconductor basics tutorial question
bioconductor basics tutorial question beginner question novice written 22 days ago by rahulsachi58 • 0 • updated 21 days ago by Gordon Smyth ♦ 35k
1
vote
0
answers
79
views
0
answers
News: BioC 3.8 release schedule
news bioconductor release written 27 days ago by Valerie Obenchain ♦♦ 6.6k
5
votes
1
answer
96
views
1
answer
Design and Contrast Matrix for Linear Model. To Combine or not to Combine?
limma design and contrast matrix design matrix contrast matrix written 23 days ago by mikhael.manurung • 10 • updated 23 days ago by James W. MacDonald ♦ 48k
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