Showing : DESeq2 • reset
1
vote
1
reply
69
views
Handling multiple differential expression comparisons
DESeq2
updated 12 hours ago by 41k • written 2 days ago by ▴ 10
0
votes
6
replies
188
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 1 day ago by ★ 1.3k • written 3 days ago by ▴ 130
2
votes
3
replies
150
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 14 hours ago by ★ 4.1k • written 2 days ago by • 0
0
votes
2
replies
92
views
DESeq2 v1.35.0
DESeq2
updated 3 days ago by 41k • written 3 days ago by • 0
0
votes
2
replies
125
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
4 days ago • updated 3 days ago kcarey • 0
0
votes
3
replies
129
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 3 days ago by ★ 4.1k • written 4 days ago by • 0
0
votes
1
reply
130
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 4 days ago by ★ 4.1k • written 4 days ago by • 0
0
votes
3
replies
242
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 4 days ago by 41k • written 5 days ago by • 0
1
vote
1
reply
102
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 5 days ago by 41k • written 5 days ago by • 0
0
votes
2
replies
119
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
5 days ago • updated 2 days ago Aurora • 0
0
votes
1
reply
100
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 5 days ago by 41k • written 6 days ago by • 0
0
votes
1
reply
100
views
putting my own expression data in deseq2
DESeq2
updated 5 days ago by ★ 4.1k • written 5 days ago by • 0
3
votes
3
replies
223
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 6 days ago by ★ 4.1k • written 6 days ago by ▴ 10
0
votes
2
replies
204
views
PCA plot suggestions
DESeq2 PCAtools
updated 9 days ago by 41k • written 10 days ago by • 0
1
vote
3
replies
214
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 9 days ago by 41k • written 10 days ago by • 0
2
votes
9
replies
388
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 10 days ago by 65k • written 10 days ago by • 0
0
votes
1
reply
151
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 11 days ago by 41k • written 11 days ago by • 0
1
vote
3
replies
208
views
Different Shrunk Log2FC according with reference
DESeq2
updated 11 days ago by 41k • written 11 days ago by ▴ 20
1
vote
4
replies
319
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
11 days ago • updated 9 days ago winwater0928 • 0
3
votes
1
reply
309
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 11 days ago by 41k • written 12 days ago by ▴ 40
0
votes
8
replies
342
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 10 days ago by ★ 1.3k • written 12 days ago by • 0
3
votes
3
replies
227
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 12 days ago by 41k • written 13 days ago by • 0
0
votes
1
reply
136
views
rlog transformation
DESeq2
updated 17 days ago by 41k • written 17 days ago by • 0
0
votes
1
reply
112
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 17 days ago by 41k • written 17 days ago by • 0
1
vote
2
replies
710
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
18 days ago • updated 9 days ago ussarizona ▴ 10
0
votes
1
reply
133
views
covariate with negative and positive values
DESeq2
updated 17 days ago by 41k • written 19 days ago by • 0
0
votes
1
reply
147
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 17 days ago by ★ 4.1k • written 18 days ago by • 0
0
votes
4
replies
235
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
18 days ago • updated 15 days ago lonn • 0
0
votes
3
replies
204
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 19 days ago by 41k • written 20 days ago by ▴ 20
1
vote
2
replies
241
views
How to retrieve detailed regression results from deseq2
DESeq2
25 days ago • updated 16 days ago Weiqian ▴ 10
0
votes
4
replies
269
views
DEG with low counts
DESeq2
updated 16 days ago by 41k • written 21 days ago by • 0
0
votes
1
reply
130
views
Deseq2 Rlog transformation
DESeq2
updated 20 days ago by ★ 4.1k • written 21 days ago by • 0
1
vote
2
replies
193
views
Design Matrix within group comparison more than two groups
DESeq2
23 days ago • updated 22 days ago hemantcnaik • 0
0
votes
1
reply
132
views
Bioinformatics student
Des DESeq2
updated 23 days ago by • 0 • written 23 days ago by • 0
0
votes
1
reply
175
views
DESeq2 gives an error and R crashes
DESeq2
25 days ago • updated 24 days ago Shefali • 0
0
votes
2
replies
220
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 25 days ago by 41k • written 4 weeks ago by ▴ 30
0
votes
1
reply
162
views
IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 26 days ago by 41k • written 26 days ago by • 0
0
votes
2
replies
247
views
Regressing out batch effects
DESeq2
updated 26 days ago by 41k • written 4 weeks ago by • 0
1
vote
4
replies
478
views
DEseq2 coefficient
DESeq2 coefficient
10 weeks ago • updated 4 days ago JKim • 0
0
votes
7
replies
422
views
DESeq filtering specific to contrasts
DESeq2
updated 16 days ago by 41k • written 11 weeks ago by • 0
0
votes
4
replies
601
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 19 days ago by 41k • written 6 months ago by • 0
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 18 days ago by • 0 • written 10 months ago by • 0
6
votes
19
replies
2.5k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 5 days ago by • 0 • written 4.6 years ago by ▴ 10
2
votes
5
replies
746
views
DESeq2 setting significant p-value
DESeq2
updated 16 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 17 days ago by • 0 • written 8.8 years ago by ▴ 30
45 results • Page 1 of 1
Recent ...
Replies
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p- by Gordon Smyth 50k
Please ask you own question. Inserting your own dataset into someone else's question like this is very impolite. I have already answered m…
Comment: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
limma most certainly is available. It installs in R 4.4.0 and Bioc 3.19 with no issues at all. If you're having trouble with Bioc installa…
Comment: package goseq seems to be not available on the latest version of R by Patrycja ▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p- by Chris • 0
Thanks Gordon for the advice! I ran fgsea, gsva and camera(), the most significant pathways are different. For the purpose of finding pathw…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
Check the number of bootstrapped data per chromosome compared to the original, and then you can also look at its distribution. For this it'…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
package goseq seems to be not available on the latest version of R
Awards • All
Scholar to ATpoint ★ 4.1k
Popular Question to Ben ▴ 50
Popular Question to Sam ▴ 10
Popular Question to Gordon Smyth 50k
Popular Question to Zainab ▴ 10
Locations • All
United States, just now
Sweden, just now
WEHI, Melbourne, Australia, 2 minutes ago
UPF, Barcelona, Spain, 3 minutes ago
France, 8 minutes ago
Traffic: 601 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