Showing : DESEq2 • reset
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 24 days ago by • 0 • written 8.8 years ago by ▴ 30
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 12 days ago by • 0 • written 4.6 years ago by ▴ 10
0
votes
2
replies
1.5k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2 SpikeIn Normalization
updated 3 days ago by • 0 • written 15 months ago by ▴ 10
2
votes
5
replies
1.2k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 26 days ago by • 0 • written 11 months ago by • 0
2
votes
5
replies
776
views
DESeq2 setting significant p-value
DESeq2
updated 23 days ago by 42k • written 5.0 years ago by ▴ 10
1
vote
2
replies
725
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
25 days ago • updated 16 days ago ussarizona ▴ 10
0
votes
4
replies
613
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 26 days ago by 42k • written 6 months ago by • 0
1
vote
4
replies
499
views
DEseq2 coefficient
DESeq2 coefficient
11 weeks ago • updated 11 days ago JKim • 0
0
votes
7
replies
436
views
DESeq filtering specific to contrasts
DESeq2
updated 23 days ago by 42k • written 12 weeks ago by • 0
2
votes
9
replies
408
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 17 days ago by 65k • written 18 days ago by • 0
0
votes
8
replies
365
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 18 days ago by ★ 1.4k • written 19 days ago by • 0
1
vote
4
replies
345
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
19 days ago • updated 17 days ago winwater0928 • 0
3
votes
1
reply
319
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 19 days ago by 42k • written 19 days ago by ▴ 40
2
votes
7
replies
289
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
5 days ago • updated 2 days ago sajadahmad41454 • 0
0
votes
3
replies
281
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 11 days ago by 42k • written 12 days ago by • 0
0
votes
4
replies
280
views
DEG with low counts
DESeq2
updated 24 days ago by 42k • written 28 days ago by • 0
1
vote
3
replies
276
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 5 days ago by ★ 4.1k • written 11 days ago by • 0
3
votes
3
replies
255
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 14 days ago by ★ 4.1k • written 14 days ago by ▴ 10
0
votes
6
replies
255
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 9 days ago by ★ 1.4k • written 10 days ago by ▴ 130
1
vote
2
replies
250
views
How to retrieve detailed regression results from deseq2
DESeq2
4 weeks ago • updated 23 days ago Weiqian ▴ 10
0
votes
4
replies
248
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
25 days ago • updated 23 days ago lonn • 0
1
vote
3
replies
239
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 17 days ago by 42k • written 17 days ago by • 0
3
votes
3
replies
235
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 20 days ago by 42k • written 20 days ago by • 0
1
vote
3
replies
226
views
Different Shrunk Log2FC according with reference
DESeq2
updated 19 days ago by 42k • written 19 days ago by ▴ 20
2
votes
3
replies
220
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 8 days ago by ★ 4.1k • written 9 days ago by • 0
0
votes
2
replies
220
views
PCA plot suggestions
DESeq2 PCAtools
updated 16 days ago by 42k • written 18 days ago by • 0
0
votes
3
replies
213
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 27 days ago by 42k • written 27 days ago by ▴ 20
0
votes
3
replies
192
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 11 days ago by ★ 4.1k • written 11 days ago by • 0
0
votes
2
replies
185
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
11 days ago • updated 10 days ago kcarey • 0
0
votes
1
reply
162
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 18 days ago by 42k • written 18 days ago by • 0
0
votes
1
reply
157
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 25 days ago by ★ 4.1k • written 26 days ago by • 0
1
vote
1
reply
154
views
Handling multiple differential expression comparisons
DESeq2
updated 8 days ago by 42k • written 9 days ago by ▴ 10
0
votes
2
replies
149
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
13 days ago • updated 10 days ago Aurora • 0
0
votes
1
reply
147
views
rlog transformation
DESeq2
updated 24 days ago by 42k • written 25 days ago by • 0
1
vote
1
reply
140
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 13 days ago by 42k • written 13 days ago by • 0
0
votes
2
replies
139
views
DESeq2 v1.35.0
DESeq2
updated 10 days ago by 42k • written 10 days ago by • 0
0
votes
1
reply
139
views
covariate with negative and positive values
DESeq2
updated 24 days ago by 42k • written 26 days ago by • 0
0
votes
1
reply
138
views
Deseq2 Rlog transformation
DESeq2
updated 28 days ago by ★ 4.1k • written 29 days ago by • 0
0
votes
1
reply
125
views
putting my own expression data in deseq2
DESeq2
updated 13 days ago by ★ 4.1k • written 13 days ago by • 0
0
votes
1
reply
125
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 13 days ago by 42k • written 13 days ago by • 0
0
votes
1
reply
119
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 24 days ago by 42k • written 25 days ago by • 0
0
votes
1
reply
81
views
Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 3 days ago by ★ 4.1k • written 3 days ago by • 0
0
votes
1
reply
72
views
normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 4 days ago by ★ 4.1k • written 4 days ago by • 0
43 results • Page 1 of 1
Recent ...
Replies
Comment: ChAMP installation issue by shepherl 3.9k
Without showing the commands you tried and the full output including error it is impossible to help. Please provide additional information…
Answer: Gene set enrichment analysis by Guido Hooiveld ★ 3.9k
No, that is not possible. The idea of gene set enrichment analysis (GSEA) is that it checks which gene sets (pathways, GO categories) are e…
Comment: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by zzrammal • 0
thank you for your response. The problem is resolved. When i did a fit for the linear model i put NULL for the design fit <- lmFit(count_…
Comment: More regions in union when increasing DBA$config$mergeOverlap by Ziliang • 0
I am so confused and frustrated learning to use this software. Isn't how you merge the peaksets one of the most important steps for the com…
Answer: SingleR Label.Ont by Denis • 0
[Jackpot City Casino][1] is the perfect option when looking for an online casino in Canada for an exciting vacation and huge winnings that …
Votes
A: DEXSeq time course design
using variable in design formula
differential expression for Single-cell RNAseq data using edgeR
Why p value inconsistent when using different number of pathway score?
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Awards • All
Popular Question to Gordon Smyth 50k
Popular Question to maria.soler • 0
Popular Question to Pietro ▴ 40
Popular Question to neilzhao ▴ 30
Popular Question to ATpoint ★ 4.1k
Locations • All
United Kingdom, 1 minute ago
Belgium, 1 minute ago
United States, 2 minutes ago
Spain, 13 minutes ago
France, 17 minutes ago
Traffic: 809 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