Showing : degs • reset
5
votes
3
replies
29k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 6.6 years ago by ▴ 30
0
votes
3
replies
1.0k
views
code syntax for DESeq2 to derive DEGs from a complicated contrast or interaction contrast?
DESeq2 Complicated.contrast DEGs
updated 3.0 years ago by 43k • written 3.0 years ago by • -60
-6
votes
4
replies
1.2k
views
is it possible and reasonable for edgeR to derive DEGs from a complicated contrast or contrast of contrast?
complicated.contrast edgeR DEGs
3.0 years ago Mike • -60
2
votes
3
replies
1.3k
views
Classic or GLM approach in edgeR, Why do I got less DEG in GLM approach?
edgeR DEGs
updated 3.4 years ago by 52k • written 3.4 years ago by • 0
0
votes
2
replies
1.2k
views
Extend comparisons between two groups to more groups in DESEQ2
edgeR DEGs DESEQ2 RNASeqData
3.6 years ago Raito92 ▴ 60
0
votes
3
replies
1.4k
views
EdgeR question: why I got discrepancy results for DEGs when using different ways setting up the models
RNAseq edgeR DEGs
updated 3.5 years ago by 52k • written 4.1 years ago by ▴ 380
0
votes
20
replies
3.4k
views
DESeq2 question: why I got discrepancy results for DEGs when using different ways setting up the models
DESeq2 DEGs
4.2 years ago • updated 4.1 years ago Ming ▴ 380
2
votes
1
reply
9.0k
views
EnhancedVolcano Label Question
RNASeq EnhancedVolcano DEGs
updated 4.2 years ago by ★ 4.0k • written 4.2 years ago by • 0
0
votes
2
replies
1.4k
views
Deseq2 cooks filter for 2 replicates x 3 replicates
DESeq2 Nullcook'svalues 2x3 DEGs
4.4 years ago andreia ▴ 10
4
votes
5
replies
2.0k
views
DEseq2 results
heatmaps DEGs PCA
updated 4.5 years ago by ★ 4.0k • written 4.5 years ago by • 0
2
votes
2
replies
1.4k
views
Design formula for pairwise comparison of experimental setup with multiple factors
DEGs DESeq2
4.7 years ago 2021yearsold • 0
0
votes
1
reply
1.2k
views
mircomb analysis from deg's list
mircomb mrna mirna degs interaction
5.2 years ago andreia ▴ 10
0
votes
2
replies
1.1k
views
mirna-mrna interation mircomb (from DEGs and DEMs lists)
deseq2 mircomb degs dems
updated 5.2 years ago by 43k • written 5.2 years ago by ▴ 10
0
votes
1
reply
1.2k
views
compareCluster error: On clusterProfiler DEGs enrichments analysis
clusterProfiler Bioconductor R DEGs
5.2 years ago tpm • 0
3
votes
2
replies
3.6k
views
How to deal with elimination of genes when using filterByExpr function?
edger DEGs normalization
updated 5.6 years ago by 52k • written 5.6 years ago by ▴ 10
2
votes
4
replies
1.4k
views
How to make grouping and contrast for multfactor design?
edger DEGs
5.7 years ago • updated 5.6 years ago anikng ▴ 10
2
votes
3
replies
1.5k
views
How to correctly set up the design in DESeq2 for RRPP?
deseq2 rrpp DEGs RNAseq
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
0
votes
2
replies
5.3k
views
Heatmap of selected genes
heatmap DEGs RNAseq DESeq2
updated 6.1 years ago by ▴ 280 • written 6.1 years ago by • 0
4
votes
3
replies
1.5k
views
Differential profile for only one normal - tumor pair
edger degs paired design
updated 7.2 years ago by 52k • written 7.2 years ago by ▴ 10
3
votes
5
replies
2.7k
views
DEGs of microarray Data and hierarchical clustering and visualizing using heatmap
limma heatmap DEGs
updated 7.6 years ago by 52k • written 7.6 years ago by ▴ 30
3
votes
1
reply
1.4k
views
Common dispersion value using edgeR for DEGs analysis
edgeR DEGS common disperion
updated 8.1 years ago by ★ 29k • written 8.1 years ago by • 0
6
votes
4
replies
3.4k
views
Identification of DEGs through limma analysis
limma microarray DEGs p values lfc
8.2 years ago rkp • 0
22 results • Page 1 of 1
Recent ...
Replies
Comment: WGCNA analysis on RNAseq and proteoimcs data by sum31278 • 0
Hi sagigordon, Can you share how you performed WGCNA analysis for proteomics data? Thanks
Comment: European Bioconductor Conference 2023 planning by inadequate.peacock.iiag • 0
I once faced a dilemma similar to this when coordinating a smaller local event; despite initial hesitation, I learned invaluable skills and…
Comment: ROAST compare results with complex design by Gordon Smyth 52k
It's also worth pointing out that the syntax for `camera` and `mroast` is the same, so I wonder how OP did the earlier `camera` analysis.
Answer: ROAST compare results with complex design by James W. MacDonald 68k
You are specifying that the last column of your design should be used as the contrast. You should instead use `contrast[,1]`, which will us…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Yes. You can infer that by figuring out what each coefficient measures. Here is your design matrix: ``` > targets ID Name phase G…
Votes
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Awards • All
Popular Question to sum31278 • 0
Popular Question to Gordon Smyth 52k
Popular Question to boczniak767 ▴ 740
Popular Question to Young Tae • 0
Popular Question to Robert Castelo ★ 3.4k
Locations • All
Barcelona, Spain, 1 minute ago
WEHI, Melbourne, Australia, 8 minutes ago
United States, 16 minutes ago
Spain, 19 minutes ago
United States, 1 hour ago
Traffic: 813 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6