Showing : DESeq2 • reset
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 13 days ago by • 0 • written 8.8 years ago by ▴ 30
6
votes
19
replies
2.4k
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 • 0 • written 4.6 years ago by ▴ 10
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 15 days ago by • 0 • written 10 months ago by • 0
2
votes
5
replies
730
views
DESeq2 setting significant p-value
DESeq2
updated 12 days ago by 41k • written 5.0 years ago by ▴ 10
1
vote
2
replies
690
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
14 days ago • updated 5 days ago ussarizona ▴ 10
0
votes
4
replies
591
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 15 days ago by 41k • written 6 months ago by • 0
1
vote
4
replies
446
views
DEseq2 coefficient
DESeq2 coefficient
9 weeks ago • updated 18 hours ago JKim • 0
1
vote
6
replies
418
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 28 days ago by 41k • written 28 days ago by • 0
0
votes
7
replies
400
views
DESeq filtering specific to contrasts
DESeq2
updated 12 days ago by 41k • written 10 weeks ago by • 0
2
votes
9
replies
339
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 6 days ago by 65k • written 7 days ago by • 0
0
votes
8
replies
321
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 7 days ago by ★ 1.3k • written 8 days ago by • 0
1
vote
4
replies
297
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
8 days ago • updated 6 days ago winwater0928 • 0
3
votes
1
reply
293
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 8 days ago by 41k • written 8 days ago by ▴ 40
0
votes
4
replies
257
views
DEG with low counts
DESeq2
updated 13 days ago by 41k • written 17 days ago by • 0
0
votes
4
replies
251
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 29 days ago by 41k • written 4 weeks ago by • 0
1
vote
2
replies
237
views
How to retrieve detailed regression results from deseq2
DESeq2
21 days ago • updated 12 days ago Weiqian ▴ 10
0
votes
2
replies
233
views
Regressing out batch effects
DESeq2
updated 22 days ago by 41k • written 27 days ago by • 0
0
votes
4
replies
225
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
14 days ago • updated 12 days ago lonn • 0
0
votes
2
replies
213
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 22 days ago by 41k • written 27 days ago by ▴ 30
3
votes
3
replies
210
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 8 days ago by 41k • written 9 days ago by • 0
0
votes
3
replies
203
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 16 hours ago by 41k • written 1 day ago by • 0
1
vote
3
replies
199
views
Different Shrunk Log2FC according with reference
DESeq2
updated 8 days ago by 41k • written 8 days ago by ▴ 20
0
votes
3
replies
199
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 16 days ago by 41k • written 16 days ago by ▴ 20
3
votes
3
replies
193
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 3 days ago by ★ 4.1k • written 3 days ago by ▴ 10
1
vote
2
replies
188
views
Design Matrix within group comparison more than two groups
DESeq2
19 days ago hemantcnaik • 0
1
vote
3
replies
184
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 6 days ago by 41k • written 6 days ago by • 0
0
votes
2
replies
179
views
PCA plot suggestions
DESeq2 PCAtools
updated 5 days ago by 41k • written 7 days ago by • 0
0
votes
1
reply
172
views
DESeq2 gives an error and R crashes
DESeq2
21 days ago • updated 20 days ago Shefali • 0
0
votes
2
replies
166
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
29 days ago michelafrancesconi8 • 0
1
vote
1
reply
160
views
DESeq2 - Missing values in count matrix
DESeq2
updated 27 days ago by 65k • written 27 days ago by • 0
0
votes
1
reply
157
views
IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 22 days ago by 41k • written 22 days ago by • 0
0
votes
2
replies
157
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 26 days ago by 65k • written 26 days ago by • 0
1
vote
1
reply
148
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
29 days ago Layal • 0
0
votes
1
reply
137
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 14 days ago by ★ 4.1k • written 15 days ago by • 0
0
votes
1
reply
129
views
Bioinformatics student
Des DESeq2
updated 19 days ago by • 0 • written 19 days ago by • 0
0
votes
1
reply
127
views
covariate with negative and positive values
DESeq2
updated 13 days ago by 41k • written 15 days ago by • 0
0
votes
1
reply
126
views
Deseq2 Rlog transformation
DESeq2
updated 17 days ago by ★ 4.1k • written 18 days ago by • 0
0
votes
1
reply
125
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 7 days ago by 41k • written 7 days ago by • 0
0
votes
1
reply
120
views
rlog transformation
DESeq2
updated 13 days ago by 41k • written 14 days ago by • 0
0
votes
1
reply
102
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 13 days ago by 41k • written 14 days ago by • 0
0
votes
1
reply
90
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 16 hours ago by ★ 4.1k • written 16 hours ago by • 0
0
votes
1
reply
82
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 1 day ago by 41k • written 2 days ago by • 0
0
votes
1
reply
78
views
putting my own expression data in deseq2
DESeq2
updated 2 days ago by ★ 4.1k • written 2 days ago by • 0
1
vote
1
reply
76
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 1 day ago by 41k • written 2 days ago by • 0
0
votes
1
reply
67
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
updated 1 day ago by 41k • written 2 days ago by • 0
0
votes
3
replies
65
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 2 hours ago by ★ 4.1k • written 14 hours ago by • 0
0
votes
1
reply
36
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
updated 3 hours ago by ★ 4.1k • written 14 hours ago by • 0
47 results • Page 1 of 1
Recent ...
Replies
Comment: Differences in differential analysis methods for RNA-Seq by ATpoint ★ 4.1k
> I am just re-processing due to being uncertain about how they used the edgeR analysis to reach gene level edgeR devs published something…
Comment: Differences in differential analysis methods for RNA-Seq by james.zhang20 • 0
Thanks for the explanations, it has helped clarify some things. Unfortunately, I am working from an early access public dataset (https://do…
Comment: Deseq2 and Normalization of RNA sequencing data by ATpoint ★ 4.1k
There is no expectation of normality that is realistic in terms of expression level. Levels are widely different between genes, and counts …
Comment: Differences in differential analysis methods for RNA-Seq by ATpoint ★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position) by Yveto • 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
Awards • All
Popular Question to rohitsatyam102 ▴ 20
Popular Question to shepherl 3.8k
Popular Question to siajunren • 0
Scholar to Rory Stark ★ 5.2k
Popular Question to tangming2005 ▴ 190
Locations • All
Sweden, just now
India, 3 minutes ago
United Kingdom, 9 minutes ago
France, 15 minutes ago
UK, 18 minutes ago
Traffic: 863 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