Showing : deseq2 • reset
1
vote
1
reply
104
views
Handling multiple differential expression comparisons
DESeq2
updated 2 days ago by 42k • written 3 days ago by ▴ 10
2
votes
3
replies
180
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 2 days ago by ★ 4.1k • written 3 days ago by • 0
0
votes
6
replies
220
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 3 days ago by ★ 1.3k • written 4 days ago by ▴ 130
0
votes
2
replies
128
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
7 days ago • updated 4 days ago Aurora • 0
0
votes
2
replies
145
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
5 days ago • updated 4 days ago kcarey • 0
0
votes
2
replies
111
views
DESeq2 v1.35.0
DESeq2
updated 4 days ago by 42k • written 4 days ago by • 0
0
votes
3
replies
146
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 5 days ago by ★ 4.1k • written 5 days ago by • 0
0
votes
3
replies
255
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 5 days ago by 42k • written 6 days ago by • 0
0
votes
1
reply
152
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 5 days ago by • 0
1
vote
4
replies
481
views
DEseq2 coefficient
DESeq2 coefficient
10 weeks ago • updated 5 days ago JKim • 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 6 days ago by • 0 • written 4.6 years ago by ▴ 10
1
vote
1
reply
115
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 7 days ago by 42k • written 7 days ago by • 0
0
votes
1
reply
107
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 7 days ago by 42k • written 7 days ago by • 0
0
votes
1
reply
112
views
putting my own expression data in deseq2
DESeq2
updated 7 days ago by ★ 4.1k • written 7 days ago by • 0
3
votes
3
replies
241
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 8 days ago by ★ 4.1k • written 8 days ago by ▴ 10
0
votes
2
replies
214
views
PCA plot suggestions
DESeq2 PCAtools
updated 10 days ago by 42k • written 12 days ago by • 0
1
vote
2
replies
716
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
20 days ago • updated 11 days ago ussarizona ▴ 10
1
vote
3
replies
226
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 11 days ago by 42k • written 11 days ago by • 0
1
vote
4
replies
334
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
13 days ago • updated 11 days ago winwater0928 • 0
2
votes
9
replies
392
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 11 days ago by 65k • written 12 days ago by • 0
0
votes
8
replies
354
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 12 days ago by ★ 1.3k • written 13 days ago by • 0
0
votes
1
reply
155
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 12 days ago by 42k • written 12 days ago by • 0
1
vote
3
replies
216
views
Different Shrunk Log2FC according with reference
DESeq2
updated 13 days ago by 42k • written 13 days ago by ▴ 20
3
votes
1
reply
315
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 13 days ago by 42k • written 13 days ago by ▴ 40
3
votes
3
replies
230
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 14 days ago by 42k • written 14 days ago by • 0
0
votes
4
replies
240
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
20 days ago • updated 17 days ago lonn • 0
1
vote
2
replies
245
views
How to retrieve detailed regression results from deseq2
DESeq2
26 days ago • updated 17 days ago Weiqian ▴ 10
0
votes
7
replies
423
views
DESeq filtering specific to contrasts
DESeq2
updated 17 days ago by 42k • written 11 weeks ago by • 0
2
votes
5
replies
756
views
DESeq2 setting significant p-value
DESeq2
updated 18 days ago by 42k • written 5.0 years ago by ▴ 10
0
votes
4
replies
270
views
DEG with low counts
DESeq2
updated 18 days ago by 42k • written 22 days ago by • 0
0
votes
1
reply
139
views
rlog transformation
DESeq2
updated 18 days ago by 42k • written 19 days ago by • 0
0
votes
1
reply
113
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 18 days ago by 42k • written 19 days ago by • 0
0
votes
1
reply
135
views
covariate with negative and positive values
DESeq2
updated 18 days ago by 42k • written 20 days ago by • 0
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 18 days ago by • 0 • written 8.8 years ago by ▴ 30
0
votes
1
reply
150
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 19 days ago by ★ 4.1k • written 20 days ago by • 0
2
votes
5
replies
1.2k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 20 days ago by • 0 • written 10 months ago by • 0
0
votes
4
replies
603
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 20 days ago by 42k • written 6 months ago by • 0
0
votes
3
replies
207
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 21 days ago by 42k • written 22 days ago by ▴ 20
0
votes
1
reply
133
views
Deseq2 Rlog transformation
DESeq2
updated 22 days ago by ★ 4.1k • written 23 days ago by • 0
1
vote
2
replies
198
views
Design Matrix within group comparison more than two groups
DESeq2
24 days ago hemantcnaik • 0
0
votes
1
reply
136
views
Bioinformatics student
Des DESeq2
updated 24 days ago by • 0 • written 24 days ago by • 0
0
votes
1
reply
178
views
DESeq2 gives an error and R crashes
DESeq2
26 days ago • updated 25 days ago Shefali • 0
0
votes
2
replies
223
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 27 days ago by 42k • written 4 weeks ago by ▴ 30
0
votes
1
reply
166
views
IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 27 days ago by 42k • written 27 days ago by • 0
0
votes
2
replies
249
views
Regressing out batch effects
DESeq2
updated 27 days ago by 42k • written 4 weeks ago by • 0
45 results • Page 1 of 1
Recent ...
Replies
Answer: meffil.snp.concordance by James W. MacDonald 65k
This support site is meant to help people with technical questions about Bioconductor packages. The `meffil` package is not Bioconductor, n…
Answer: minfi latest update for EPIC V2 chip by James W. MacDonald 65k
Zuguang Gu submitted both of those packages as part of the current release, and I submitted a PR for `minfi` so it will now distinguish the…
Answer: Recovering my account credentials on Bioconductor by shepherl 3.9k
As we will need to exchange some information can you please contact me at bioconductorcoreteam@gmail.com and I can better assist you. Che…
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Hervé Pagès 16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Votes
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
Comment: minfi support of illumina Infinium methylationEPIC v2.0
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
Awards • All
Popular Question to Gordon Smyth 50k
Popular Question to WouterDeCoster ▴ 130
Scholar to Michael Love 42k
Popular Question to Malcolm Cook ★ 1.6k
Popular Question to priyanka.m • 0
Locations • All
India, 1 minute ago
United States, 2 minutes ago
France, 2 minutes ago
Sweden, 19 minutes ago
Switzerland, 27 minutes ago
Traffic: 952 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