Showing : DESeq2 • reset
1
vote
8
replies
132
views
Slightly different count plots from R and spreadsheet
DESeq2 ggplot2
20 hours ago • updated 12 hours ago boczniak767 ▴ 720
1
vote
3
replies
135
views
LRT, more than two conditions and pairwise comparisons
DESeq2
updated 2 days ago by 66k • written 3 days ago by ▴ 720
0
votes
6
replies
594
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
5 days ago • updated 2 days ago Ken C • 0
2
votes
4
replies
214
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 2 days ago by 42k • written 5 days ago by • 0
4
votes
9
replies
307
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 6 days ago by ★ 4.1k • written 8 days ago by • 0
0
votes
3
replies
150
views
Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 7 days ago by 42k • written 8 days ago by • 0
0
votes
1
reply
117
views
normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 8 days ago by 42k • written 9 days ago by • 0
0
votes
8
replies
551
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 8 days ago by ▴ 30 • written 9 days ago by • 0
1
vote
2
replies
269
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2 eigencorplot PCAtools
9 days ago • updated 6 days ago BioinfGuru ▴ 30
0
votes
1
reply
192
views
Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 13 days ago by ★ 4.1k • written 13 days ago by • 0
0
votes
1
reply
119
views
normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 14 days ago by ★ 4.1k • written 14 days ago by • 0
2
votes
7
replies
442
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
15 days ago • updated 11 days ago sajadahmad41454 • 0
1
vote
1
reply
198
views
Handling multiple differential expression comparisons
DESeq2
updated 17 days ago by 42k • written 19 days ago by ▴ 10
0
votes
6
replies
312
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 19 days ago by ★ 1.4k • written 20 days ago by ▴ 130
2
votes
3
replies
267
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 18 days ago by ★ 4.1k • written 19 days ago by • 0
0
votes
2
replies
180
views
DESeq2 v1.35.0
DESeq2
updated 20 days ago by 42k • written 20 days ago by • 0
0
votes
2
replies
219
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
21 days ago • updated 20 days ago kcarey • 0
0
votes
3
replies
235
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 20 days ago by ★ 4.1k • written 21 days ago by • 0
1
vote
3
replies
318
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 15 days ago by ★ 4.1k • written 21 days ago by • 0
0
votes
3
replies
309
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 21 days ago by 42k • written 22 days ago by • 0
1
vote
1
reply
161
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 22 days ago by 42k • written 22 days ago by • 0
0
votes
2
replies
175
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
23 days ago • updated 20 days ago Aurora • 0
0
votes
1
reply
142
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 22 days ago by 42k • written 23 days ago by • 0
0
votes
1
reply
142
views
putting my own expression data in deseq2
DESeq2
updated 22 days ago by ★ 4.1k • written 23 days ago by • 0
3
votes
3
replies
278
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 24 days ago by ★ 4.1k • written 24 days ago by ▴ 10
0
votes
2
replies
231
views
PCA plot suggestions
DESeq2 PCAtools
updated 26 days ago by 42k • written 28 days ago by • 0
1
vote
3
replies
261
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 26 days ago by 42k • written 27 days ago by • 0
2
votes
9
replies
441
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 27 days ago by 66k • written 27 days ago by • 0
0
votes
1
reply
169
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 28 days ago by 42k • written 28 days ago by • 0
1
vote
3
replies
243
views
Different Shrunk Log2FC according with reference
DESeq2
updated 28 days ago by 42k • written 29 days ago by ▴ 20
1
vote
4
replies
365
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
29 days ago • updated 27 days ago winwater0928 • 0
3
votes
1
reply
334
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 29 days ago by 42k • written 29 days ago by ▴ 40
0
votes
8
replies
407
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 28 days ago by ★ 1.4k • written 29 days ago by • 0
3
votes
3
replies
260
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 29 days ago by 42k • written 4 weeks ago by • 0
0
votes
1
reply
160
views
rlog transformation
DESeq2
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
0
votes
1
reply
133
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 4 weeks ago by 42k • written 5 weeks ago by • 0
1
vote
2
replies
764
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
5 weeks ago • updated 26 days ago Patadù ▴ 10
0
votes
1
reply
151
views
covariate with negative and positive values
DESeq2
updated 4 weeks ago by 42k • written 5 weeks ago by • 0
0
votes
1
reply
171
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 4 weeks ago by ★ 4.1k • written 5 weeks ago by • 0
0
votes
4
replies
273
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
5 weeks ago • updated 4 weeks ago lonn • 0
0
votes
3
replies
237
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 5 weeks ago by 42k • written 5 weeks ago by ▴ 20
1
vote
2
replies
272
views
How to retrieve detailed regression results from deseq2
DESeq2
6 weeks ago • updated 4 weeks ago Weiqian ▴ 10
0
votes
4
replies
296
views
DEG with low counts
DESeq2
updated 4 weeks ago by 42k • written 5 weeks ago by • 0
0
votes
1
reply
154
views
Deseq2 Rlog transformation
DESeq2
updated 5 weeks ago by ★ 4.1k • written 5 weeks ago by • 0
1
vote
2
replies
217
views
Design Matrix within group comparison more than two groups
DESeq2
5 weeks ago hemantcnaik • 0
0
votes
1
reply
155
views
Bioinformatics student
Des DESeq2
updated 5 weeks ago by • 0 • written 5 weeks ago by • 0
0
votes
1
reply
202
views
DESeq2 gives an error and R crashes
DESeq2
6 weeks ago • updated 5 weeks ago Shefali • 0
0
votes
2
replies
250
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 6 weeks ago by 42k • written 6 weeks ago by ▴ 40
0
votes
1
reply
196
views
IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 6 weeks ago by 42k • written 6 weeks ago by • 0
0
votes
2
replies
267
views
Regressing out batch effects
DESeq2
updated 6 weeks ago by 42k • written 6 weeks ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Get gene symbols for a set of hg19 coordinates by ATpoint ★ 4.1k
Simply download a GTF file (for example from GENCODE) matching the current genome and/or annotation version you are using in your project a…
Comment: Not able to install any Bioconductor 3.18 package [unable to access index] by ATpoint ★ 4.1k
Try the mirror suggestion for now: https://support.bioconductor.org/p/9153734/#9153755
Comment: unable to access bioconductor packages - qvalue installation failed... by ATpoint ★ 4.1k
Seems to be a general problem at the moment, can reproduce. The the mirror suggestion here: https://support.bioconductor.org/p/9153734/#915…
Comment: Running ENmix with mouse methylation manifest: readidat error - Error in readman by Karosham.Reddy • 0
Thank you for the suggestion the ENmix version is using is ENmix_1.38.01. I tried your suggested code, R identified the idat files but sti…
Comment: pathview error by Guido Hooiveld ★ 4.0k
> Will removing the NA values help solve the problem? Did you try? And, FWIW, in the cases I had ensembl-based RNA-seq datasets I removed…
Votes
Comment: recount3 problem downloading data from source sra
Not able to install any Bioconductor 3.18 package [unable to access index]
unable to access bioconductor packages - qvalue installation failed...
Not able to install any Bioconductor 3.18 package [unable to access index]
can't open mghp.osn.xsede.org
Awards • All
Popular Question to mgdrnl • 0
Popular Question to Lorena Pantano ▴ 140
Popular Question to merv ▴ 120
Popular Question to Andrew Pattison • 0
Popular Question to pcantalupo ▴ 10
Locations • All
Spain, just now
Germany, 1 minute ago
Sweden, 2 minutes ago
Singapore, 4 minutes ago
Greece, 5 minutes ago
Traffic: 815 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