Showing: differential expression • reset
Search
13
votes
3
answers
1.2k
views
6 follow
3
answers
DESeq2 1.20.0 lfcshrink function
deseq2 differential expression logfoldchange lfcthreshold lfcshrink written 13 months ago by emi.sch • 10 • updated 8 days ago by yusuf.zhc • 0
2
votes
1
answer
99
views
1
answer
Majority upregulated genes in edgeR
edger differential expression genes fold change written 22 days ago by ilovesuperheroes1993 • 0 • updated 22 days ago by Aaron Lun • 24k
1
vote
1
answer
77
views
1
answer
All Pairwise Comparisons with DESeq2 While Controlling for Batch Effects: Does Reference Level Matter?
deseq2 differential expression design batch correction written 5 weeks ago by wunderl • 20 • updated 4 weeks ago by Michael Love ♦ 24k
4
votes
1
answer
85
views
1
answer
Batch Correction: DESeq2 Linear Model vs Batch-Correction-Specific Algorithms (RUV, ComBat, ect.)
deseq2 differential expression batch correction written 5 weeks ago by wunderl • 20 • updated 4 weeks ago by Michael Love ♦ 24k
1
vote
1
answer
129
views
1
answer
RNA-Seq and edgeR: remarkable differences between cpms and fitted values
normalization edger differential expression rna-seq fitted values written 5 weeks ago by David Rengel • 70 • updated 5 weeks ago by Gordon Smyth ♦ 37k
3
votes
2
answers
124
views
2
answers
How does limma calculate the log2fc?
limma differential expression time-course analysis written 8 weeks ago by mcfarn1 • 0 • updated 8 weeks ago by Gordon Smyth ♦ 37k
1
vote
1
answer
125
views
1
answer
How to normalize RNA-seq when 50% genes are DE? (TMM)
rnaseq normalization limma differential expression tmm written 3 months ago by natalia_lt • 0 • updated 3 months ago by James W. MacDonald ♦ 50k
0
votes
0
answers
135
views
0
answers
Scran: Performing DE after cell-typle identifaction on the corrected and integrated datasets
differential expression scran single-cell mnn_correct written 4 months ago by baldissera152 • 0
4
votes
1
answer
152
views
1
answer
Limma - Using removeBatchEffect before differential expression analysis
limma differential expression batch effect written 4 months ago by jmoon1194 • 0 • updated 4 months ago by James W. MacDonald ♦ 50k
0
votes
0
answers
178
views
0
answers
Using PEER to identify hidden confounders in RNA-seq data (not working)
differential expression rna-seq peer hidden confounders written 5 months ago by rodrigo.duarte88 • 0 • updated 5 months ago by Martin Morgan ♦♦ 23k
0
votes
1
answer
201
views
1
answer
How to handle replicates and treatment conditions in TissueEnrich package
differential expression rna-seq tissueenrich tissue-specific expression written 6 months ago by andrew.oler • 0 • updated 6 months ago by Ashish Jain • 0
1
vote
1
answer
138
views
1
answer
PLAGE method fails in GSVA if an overlap between gene sets and genes in expressions is less than two
gsva differential expression gene set enrichment plage written 6 months ago by krassowski.michal • 0
2
votes
2
answers
384
views
2
answers
Get the countsFromAbundance as limma input
limma deseq2 differential expression tximport written 10 months ago by Darklings • 0 • updated 10 months ago by Gordon Smyth ♦ 37k
15
votes
1
answer
660
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 11 months ago by rory.kirchner • 60 • updated 11 months ago by Michael Love ♦ 24k
1
vote
1
answer
273
views
1
answer
Global expression shift using RUVSeq
rnaseq normalization ruvseq differential expression written 12 months ago by Leon • 0 • updated 12 months ago by davide risso • 830
1
vote
1
answer
230
views
1
answer
venDiagram after limma showing more genes after specifying up or down regulated specifically
microarray limma venn diagram differential expression venndiagram written 12 months ago by A • 40 • updated 12 months ago by James W. MacDonald ♦ 50k
4
votes
1
answer
255
views
1
answer
DE analysis when large portion of transcriptome is changed
edger ebseq differential expression rna-seq written 12 months ago by marhabaie • 0 • updated 12 months ago by Aaron Lun • 24k
0
votes
1
answer
370
views
1
answer
Deseq2 problem visualizing gene expression with batch corrected values
visualization limma deseq2 differential expression written 13 months ago by Mbosio85 • 0 • updated 12 months ago by Michael Love ♦ 24k
1
vote
1
answer
281
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 months ago by al-ash • 20 • updated 12 months ago by Michael Love ♦ 24k
0
votes
0
answers
199
views
0
answers
pair wise ballgown
differential expression ballgown written 13 months ago by zoe.ward • 0
0
votes
0
answers
245
views
0
answers
Ballgown normalisation... why are still using FPKM?
rnaseq normalization differential expression differential gene expression written 13 months ago by manuelmendoza • 0
1
vote
0
answers
302
views
0
answers
differential expression analysis with big dataset and >500 surrogate variables
sva deseq2 differential expression lrt written 14 months ago by aec • 40
0
votes
1
answer
314
views
1
answer
Interpretation of p-value plot
limma differential expression p values written 14 months ago by karlien.springael • 0 • updated 14 months ago by Gordon Smyth ♦ 37k
5
votes
2
answers
339
views
2
answers
Finding genes respond differently to treatment between many genotype comparison
edger differential expression nested design written 14 months ago by chiayi • 0 • updated 14 months ago by Gordon Smyth ♦ 37k
0
votes
1
answer
260
views
1
answer
interaction model deseq2 specific DE genes
deseq2 differential expression interaction model written 15 months ago by aec • 40 • updated 15 months ago by Michael Love ♦ 24k
<prev • 111 results • page 1 of 5 • next >
Recent...
Replies
Votes
Awards • All »
Locations • All »
  • Jakarta, Indonesia, 2 minutes ago
  • Sweden, 3 minutes ago
  • Japan, 20 minutes ago
Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 245 users visited in the last hour