Showing : DESeq2 • reset
0
votes
0
replies
7
views
PCA plot suggestions
DESeq2 PCAtools
1 hour ago Aaliya • 0
0
votes
1
reply
60
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 7 hours ago by 41k • written 11 hours ago by • 0
1
vote
3
replies
76
views
Different Shrunk Log2FC according with reference
DESeq2
updated 16 hours ago by 41k • written 20 hours ago by ▴ 20
0
votes
1
reply
61
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
updated 11 hours ago by ★ 1.3k • written 21 hours ago by • 0
2
votes
1
reply
156
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 1 day ago by 41k • written 1 day ago by ▴ 40
0
votes
7
replies
149
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
1 day ago • updated 1 hour ago Aaliya • 0
3
votes
3
replies
149
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 1 day ago by 41k • written 2 days ago by • 0
0
votes
1
reply
87
views
rlog transformation
DESeq2
updated 6 days ago by 41k • written 6 days ago by • 0
0
votes
1
reply
85
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 6 days ago by 41k • written 6 days ago by • 0
0
votes
4
replies
193
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
7 days ago • updated 4 days ago lonn • 0
0
votes
1
reply
95
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 6 days ago by 41k • written 7 days ago by • 0
0
votes
1
reply
112
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 6 days ago by ★ 4.0k • written 7 days ago by • 0
0
votes
1
reply
110
views
covariate with negative and positive values
DESeq2
updated 6 days ago by 41k • written 8 days ago by • 0
0
votes
3
replies
174
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 8 days ago by 41k • written 9 days ago by ▴ 20
0
votes
4
replies
229
views
DEG with low counts
DESeq2
updated 5 days ago by 41k • written 10 days ago by • 0
0
votes
1
reply
109
views
Deseq2 Rlog transformation
DESeq2
updated 9 days ago by ★ 4.0k • written 10 days ago by • 0
1
vote
2
replies
163
views
Design Matrix within group comparison more than two groups
DESeq2
12 days ago • updated 11 days ago hemantcnaik • 0
0
votes
1
reply
117
views
Bioinformatics student
Des DESeq2
updated 12 days ago by • 0 • written 12 days ago by • 0
0
votes
1
reply
154
views
DESeq2 gives an error and R crashes
DESeq2
14 days ago • updated 13 days ago Shefali • 0
1
vote
2
replies
217
views
How to retrieve detailed regression results from deseq2
DESeq2
14 days ago • updated 5 days ago Weiqian ▴ 10
0
votes
1
reply
137
views
IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 15 days ago by 41k • written 15 days ago by • 0
0
votes
2
replies
142
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 19 days ago by 65k • written 19 days ago by • 0
0
votes
2
replies
192
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 15 days ago by 41k • written 19 days ago by ▴ 30
0
votes
2
replies
219
views
Regressing out batch effects
DESeq2
updated 15 days ago by 41k • written 20 days ago by • 0
1
vote
1
reply
152
views
DESeq2 - Missing values in count matrix
DESeq2
updated 20 days ago by 65k • written 20 days ago by • 0
1
vote
6
replies
401
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 21 days ago by 41k • written 21 days ago by • 0
1
vote
1
reply
136
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
22 days ago • updated 21 days ago Layal • 0
0
votes
2
replies
152
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
22 days ago • updated 21 days ago michelafrancesconi8 • 0
0
votes
4
replies
229
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 22 days ago by 41k • written 23 days ago by • 0
0
votes
1
reply
142
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 27 days ago by 41k • written 27 days ago by • 0
2
votes
3
replies
324
views
PCA of different bacterial species
DESeq2
updated 28 days ago by 41k • written 29 days ago by ▴ 10
1
vote
2
replies
211
views
DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
4 weeks ago • updated 28 days ago Chanderkant Chaudhary • 0
0
votes
7
replies
406
views
DESeq2 filtering vs edgeR filtering
DESeq2
6 weeks ago • updated 29 days ago fr8712ca-s • 0
0
votes
7
replies
385
views
DESeq filtering specific to contrasts
DESeq2
updated 5 days ago by 41k • written 9 weeks ago by • 0
0
votes
4
replies
565
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 8 days ago by 41k • written 6 months ago by • 0
1
vote
8
replies
1.2k
views
DESeq2 test for synergistic vs additive effects
synergistic additive DESeq2
updated 24 days ago by ★ 13k • written 9 months ago by ▴ 10
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 7 days ago by • 0 • written 10 months ago by • 0
6
votes
16
replies
2.2k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 1 day ago by 41k • written 4.6 years ago by ▴ 10
2
votes
5
replies
695
views
DESeq2 setting significant p-value
DESeq2
updated 5 days ago by 41k • written 5.0 years ago by ▴ 10
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 6 days ago by • 0 • written 8.8 years ago by ▴ 30
40 results • Page 1 of 1
Recent ...
Replies
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by shuwangxinze1996 • 0
Hello, I used 48 cpus and 320G of memory to run this program. My bam files size are 7-9G, wonder how much CPU and memory is enough?
Comment: DESeq2 output used for PCA plot on R studio by Kevin Blighe ★ 3.9k
This comment helps.
Comment: DESeq2 output used for PCA plot on R studio by Kevin Blighe ★ 3.9k
I am not sure how your comment helps here?
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Votes
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
Awards • All
Supporter to JKim • 0
Popular Question to Gordon Smyth 50k
Popular Question to Chris • 0
Supporter to Jonathan ▴ 10
Popular Question to Bine ▴ 40
Locations • All
WEHI, Melbourne, Australia, 4 minutes ago
Colombia, 27 minutes ago
France, 48 minutes ago
United States, 1 hour ago
Singapore, 1 hour ago
Traffic: 706 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