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2
votes
2
answers
198
views
2
answers
Get the countsFromAbundance as limma input
limma deseq2 differential expression tximport written 11 weeks ago by Darklings • 0 • updated 11 weeks ago by Gordon Smyth ♦ 35k
14
votes
1
answer
364
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 3 months ago by rory.kirchner • 60 • updated 3 months ago by Michael Love ♦ 20k
1
vote
1
answer
126
views
1
answer
Global expression shift using RUVSeq
rnaseq normalization ruvseq differential expression written 4 months ago by Leon • 0 • updated 4 months ago by davide risso • 780
1
vote
1
answer
112
views
1
answer
venDiagram after limma showing more genes after specifying up or down regulated specifically
microarray limma venn diagram differential expression venndiagram written 4 months ago by A • 0 • updated 4 months ago by James W. MacDonald ♦ 48k
4
votes
1
answer
129
views
1
answer
DE analysis when large portion of transcriptome is changed
edger ebseq differential expression rna-seq written 4 months ago by marhabaie • 0 • updated 4 months ago by Aaron Lun • 21k
0
votes
1
answer
161
views
1
answer
Deseq2 problem visualizing gene expression with batch corrected values
visualization limma deseq2 differential expression written 5 months ago by Mbosio85 • 0 • updated 4 months ago by Michael Love ♦ 20k
6
votes
1
answer
360
views
1
answer
DESeq2 1.20.0 lfcshrink function
deseq2 differential expression logfoldchange lfcthreshold lfcshrink written 4 months ago by emi.sch • 0 • updated 4 months ago by Michael Love ♦ 20k
1
vote
1
answer
142
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 4 months ago by al-ash • 20 • updated 4 months ago by Michael Love ♦ 20k
0
votes
0
answers
94
views
0
answers
pair wise ballgown
differential expression ballgown written 5 months ago by zoe.ward • 0
0
votes
0
answers
118
views
0
answers
Ballgown normalisation... why are still using FPKM?
rnaseq normalization differential expression differential gene expression written 5 months ago by manuelmendoza • 0
1
vote
0
answers
166
views
0
answers
differential expression analysis with big dataset and >500 surrogate variables
sva deseq2 differential expression lrt written 6 months ago by aec • 40
0
votes
1
answer
204
views
1
answer
Interpretation of p-value plot
limma differential expression p values written 6 months ago by karlien.springael • 0 • updated 6 months ago by Gordon Smyth ♦ 35k
5
votes
2
answers
215
views
2
answers
Finding genes respond differently to treatment between many genotype comparison
edger differential expression nested design written 6 months ago by chiayi • 0 • updated 6 months ago by Gordon Smyth ♦ 35k
0
votes
1
answer
154
views
1
answer
interaction model deseq2 specific DE genes
deseq2 differential expression interaction model written 7 months ago by aec • 40 • updated 7 months ago by Michael Love ♦ 20k
6
votes
1
answer
237
views
1
answer
Fitting Gamma GLMs for examining differential expression
edger deseq2 differential expression written 8 months ago by jspmccain • 10 • updated 8 months ago by Ryan C. Thompson ♦ 7.0k
3
votes
1
answer
782
views
1
answer
Justification for collapsing technical replicates in DESeq2
rnaseq deseq2 differential expression replicate written 2.3 years ago by kieranrcampbell • 30 • updated 8 months ago by jovel_juan • 10
7
votes
1
answer
360
views
1
answer
Analysis of pathways using edgeR
rnaseq edger kegg differential expression written 8 months ago by fawazfebin • 30 • updated 8 months ago by Gordon Smyth ♦ 35k
1
vote
1
answer
360
views
1
answer
How to perform time-course differential expression with "erroneous" baseline in edgeR?
timecourse edger differential expression written 9 months ago by Enzo Castillejos • 0 • updated 9 months ago by Gordon Smyth ♦ 35k
1
vote
1
answer
726
views
1
answer
Using DESeq2 to analyse TCGA data
deseq2 differential expression tcga gene expression tcgabiolinks written 9 months ago by victor.ramos.usp • 0 • updated 9 months ago by Michael Love ♦ 20k
1
vote
2
answers
226
views
2
answers
Differential expressiong with two groups in BASiCS
bayesian differential expression single-cell basics written 9 months ago by muad.abdelhay • 10 • updated 9 months ago by CataVallejos • 10
0
votes
1
answer
221
views
1
answer
Run tweeDEseq on Flux-capacitor RPKM values
tweedeseq differential expression written 9 months ago by vrehaman • 0 • updated 9 months ago by Robert Castelo • 2.2k
0
votes
1
answer
227
views
1
answer
DESeq2, no significantly DE genes
deseq2 differential expression adjusted pvalue written 10 months ago by A • 0 • updated 10 months ago by Michael Love ♦ 20k
2
votes
1
answer
305
views
1
answer
Protein differential Expression analysis
proteomics differential expression written 10 months ago by cardin.julie • 0 • updated 10 months ago by Laurent Gatto ♦ 1.0k
0
votes
0
answers
158
views
0
answers
TCGAvisualize_EAbarplot error in TCGAbiolinks
differential expression tcgabiolinks tcgavisualize_eabarplot written 10 months ago by fawazfebin • 30
1
vote
3
answers
823
views
3
answers
DESeq2 and edgeR getting very different results
edger deseq2 differential expression written 11 months ago by audrey.o.renson • 0 • updated 11 months ago by pablo_garcia05 • 20
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