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2
votes
2
answers
142
views
2
answers
Get the countsFromAbundance as limma input
limma deseq2 differential expression tximport written 23 days ago by Darklings • 0 • updated 22 days ago by Gordon Smyth ♦ 35k
14
votes
1
answer
240
views
5 follow
1
answer
ZINB-WaVE + DESeq2 misses low-expressed, single-condition genes that look like they should be markers
deseq2 differential expression rna-seq single cell zinb-wave written 5 weeks ago by rory.kirchner • 60 • updated 5 weeks ago by Michael Love ♦ 19k
1
vote
1
answer
92
views
1
answer
Global expression shift using RUVSeq
rnaseq normalization ruvseq differential expression written 10 weeks ago by Leon • 0 • updated 10 weeks ago by davide risso • 740
1
vote
1
answer
86
views
1
answer
venDiagram after limma showing more genes after specifying up or down regulated specifically
microarray limma venn diagram differential expression venndiagram written 10 weeks ago by A • 0 • updated 10 weeks ago by James W. MacDonald ♦ 47k
4
votes
1
answer
99
views
1
answer
DE analysis when large portion of transcriptome is changed
edger ebseq differential expression rna-seq written 11 weeks ago by marhabaie • 0 • updated 11 weeks ago by Aaron Lun • 21k
0
votes
1
answer
114
views
1
answer
Deseq2 problem visualizing gene expression with batch corrected values
visualization limma deseq2 differential expression written 3 months ago by Mbosio85 • 0 • updated 12 weeks ago by Michael Love ♦ 19k
6
votes
1
answer
212
views
1
answer
DESeq2 1.20.0 lfcshrink function
deseq2 differential expression logfoldchange lfcthreshold lfcshrink written 3 months ago by emi.sch • 0 • updated 12 weeks ago by Michael Love ♦ 19k
1
vote
1
answer
99
views
1
answer
DE analysis of orthologs with varying sequence lengths using RSEM+tximport+DEseq2: normalization for sequence length?
deseq2 differential expression tximport rsem sequence length normalization written 12 weeks ago by al-ash • 10 • updated 12 weeks ago by Michael Love ♦ 19k
0
votes
0
answers
65
views
0
answers
pair wise ballgown
differential expression ballgown written 3 months ago by zoe.ward • 0
0
votes
0
answers
90
views
0
answers
Ballgown normalisation... why are still using FPKM?
rnaseq normalization differential expression differential gene expression written 3 months ago by manuelmendoza • 0
1
vote
0
answers
134
views
0
answers
differential expression analysis with big dataset and >500 surrogate variables
sva deseq2 differential expression lrt written 4 months ago by aec • 40
0
votes
1
answer
159
views
1
answer
Interpretation of p-value plot
limma differential expression p values written 4 months ago by karlien.springael • 0 • updated 4 months ago by Gordon Smyth ♦ 35k
5
votes
2
answers
179
views
2
answers
Finding genes respond differently to treatment between many genotype comparison
edger differential expression nested design written 4 months ago by chiayi • 0 • updated 4 months ago by Gordon Smyth ♦ 35k
0
votes
1
answer
129
views
1
answer
interaction model deseq2 specific DE genes
deseq2 differential expression interaction model written 5 months ago by aec • 40 • updated 5 months ago by Michael Love ♦ 19k
6
votes
1
answer
196
views
1
answer
Fitting Gamma GLMs for examining differential expression
edger deseq2 differential expression written 6 months ago by jspmccain • 10 • updated 6 months ago by Ryan C. Thompson ♦ 6.8k
3
votes
1
answer
655
views
1
answer
Justification for collapsing technical replicates in DESeq2
rnaseq deseq2 differential expression replicate written 2.2 years ago by kieranrcampbell • 30 • updated 6 months ago by jovel_juan • 10
7
votes
1
answer
295
views
1
answer
Analysis of pathways using edgeR
rnaseq edger kegg differential expression written 6 months ago by fawazfebin • 30 • updated 6 months ago by Gordon Smyth ♦ 35k
1
vote
1
answer
289
views
1
answer
How to perform time-course differential expression with "erroneous" baseline in edgeR?
timecourse edger differential expression written 7 months ago by Enzo Castillejos • 0 • updated 7 months ago by Gordon Smyth ♦ 35k
1
vote
1
answer
570
views
1
answer
Using DESeq2 to analyse TCGA data
deseq2 differential expression tcga gene expression tcgabiolinks written 7 months ago by victor.ramos.usp • 0 • updated 7 months ago by Michael Love ♦ 19k
1
vote
2
answers
196
views
2
answers
Differential expressiong with two groups in BASiCS
bayesian differential expression single-cell basics written 7 months ago by muad.abdelhay • 10 • updated 7 months ago by CataVallejos • 10
0
votes
1
answer
186
views
1
answer
Run tweeDEseq on Flux-capacitor RPKM values
tweedeseq differential expression written 7 months ago by vrehaman • 0 • updated 7 months ago by Robert Castelo • 2.2k
0
votes
1
answer
192
views
1
answer
DESeq2, no significantly DE genes
deseq2 differential expression adjusted pvalue written 8 months ago by A • 0 • updated 8 months ago by Michael Love ♦ 19k
2
votes
1
answer
241
views
1
answer
Protein differential Expression analysis
proteomics differential expression written 8 months ago by cardin.julie • 0 • updated 8 months ago by Laurent Gatto ♦ 1.0k
0
votes
0
answers
135
views
0
answers
TCGAvisualize_EAbarplot error in TCGAbiolinks
differential expression tcgabiolinks tcgavisualize_eabarplot written 8 months ago by fawazfebin • 30
1
vote
3
answers
547
views
3
answers
DESeq2 and edgeR getting very different results
edger deseq2 differential expression written 9 months ago by audrey.o.renson • 0 • updated 9 months ago by pablo_garcia05 • 20
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