Showing : DESEQ2 • reset
9
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12
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7.8k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 19 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 7 days ago by • 0 • written 4.6 years ago by ▴ 10
2
votes
5
replies
1.2k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 21 days ago by • 0 • written 10 months ago by • 0
2
votes
5
replies
762
views
DESeq2 setting significant p-value
DESeq2
updated 18 days ago by 42k • written 5.0 years ago by ▴ 10
1
vote
2
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720
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
20 days ago • updated 11 days ago ussarizona ▴ 10
0
votes
4
replies
603
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 21 days ago by 42k • written 6 months ago by • 0
1
vote
4
replies
483
views
DEseq2 coefficient
DESeq2 coefficient
10 weeks ago • updated 6 days ago JKim • 0
0
votes
7
replies
426
views
DESeq filtering specific to contrasts
DESeq2
updated 18 days ago by 42k • written 11 weeks ago by • 0
2
votes
9
replies
394
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 12 days ago by 65k • written 13 days ago by • 0
0
votes
8
replies
356
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 13 days ago by ★ 1.3k • written 14 days ago by • 0
1
vote
4
replies
338
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
14 days ago • updated 12 days ago winwater0928 • 0
3
votes
1
reply
316
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 14 days ago by 42k • written 14 days ago by ▴ 40
0
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4
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271
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DEG with low counts
DESeq2
updated 19 days ago by 42k • written 23 days ago by • 0
0
votes
3
replies
260
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 6 days ago by 42k • written 7 days ago by • 0
0
votes
2
replies
249
views
Regressing out batch effects
DESeq2
updated 28 days ago by 42k • written 4 weeks ago by • 0
1
vote
2
replies
245
views
How to retrieve detailed regression results from deseq2
DESeq2
27 days ago • updated 18 days ago Weiqian ▴ 10
0
votes
4
replies
242
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
20 days ago • updated 18 days ago lonn • 0
3
votes
3
replies
241
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 9 days ago by ★ 4.1k • written 9 days ago by ▴ 10
3
votes
3
replies
231
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 14 days ago by 42k • written 15 days ago by • 0
1
vote
3
replies
227
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 11 days ago by 42k • written 12 days ago by • 0
0
votes
6
replies
225
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 4 days ago by ★ 1.3k • written 5 days ago by ▴ 130
0
votes
2
replies
223
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 28 days ago by 42k • written 4 weeks ago by ▴ 30
1
vote
3
replies
222
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 4 hours ago by ★ 4.1k • written 6 days ago by • 0
1
vote
3
replies
217
views
Different Shrunk Log2FC according with reference
DESeq2
updated 13 days ago by 42k • written 14 days ago by ▴ 20
0
votes
2
replies
214
views
PCA plot suggestions
DESeq2 PCAtools
updated 11 days ago by 42k • written 13 days ago by • 0
0
votes
3
replies
209
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 21 days ago by 42k • written 22 days ago by ▴ 20
1
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2
replies
199
views
Design Matrix within group comparison more than two groups
DESeq2
25 days ago hemantcnaik • 0
2
votes
3
replies
186
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 3 days ago by ★ 4.1k • written 4 days ago by • 0
0
votes
1
reply
178
views
DESeq2 gives an error and R crashes
DESeq2
27 days ago • updated 26 days ago Shefali • 0
0
votes
1
reply
167
views
IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 28 days ago by 42k • written 28 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 13 days ago by 42k • written 13 days ago by • 0
0
votes
3
replies
155
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 6 days ago by ★ 4.1k • written 6 days ago by • 0
0
votes
2
replies
151
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
6 days ago • updated 5 days ago kcarey • 0
0
votes
1
reply
151
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 20 days ago by ★ 4.1k • written 20 days ago by • 0
0
votes
1
reply
139
views
rlog transformation
DESeq2
updated 19 days ago by 42k • written 20 days ago by • 0
0
votes
1
reply
137
views
Bioinformatics student
Des DESeq2
updated 25 days ago by • 0 • written 25 days ago by • 0
0
votes
1
reply
135
views
covariate with negative and positive values
DESeq2
updated 19 days ago by 42k • written 21 days ago by • 0
0
votes
1
reply
133
views
Deseq2 Rlog transformation
DESeq2
updated 23 days ago by ★ 4.1k • written 24 days ago by • 0
0
votes
2
replies
130
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
8 days ago • updated 5 days ago Aurora • 0
1
vote
1
reply
120
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
2
replies
115
views
DESeq2 v1.35.0
DESeq2
updated 5 days ago by 42k • written 5 days ago by • 0
0
votes
1
reply
114
views
putting my own expression data in deseq2
DESeq2
updated 8 days ago by ★ 4.1k • written 8 days ago by • 0
1
vote
1
reply
113
views
Handling multiple differential expression comparisons
DESeq2
updated 3 days ago by 42k • written 4 days ago by ▴ 10
0
votes
1
reply
113
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 19 days ago by 42k • written 20 days ago by • 0
0
votes
1
reply
110
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 7 days ago by 42k • written 8 days ago by • 0
0
votes
1
reply
24
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
updated 3 hours ago by ★ 4.1k • written 4 hours ago by • 0
46 results • Page 1 of 1
Recent ...
Replies
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Mike Smith ★ 6.5k
The other answers here are all good and demonstrate the issue with floating point comparisons nicely. I'd like to add that your particular…
Comment: More regions in union when increasing DBA$config$mergeOverlap by Ian D. ▴ 70
Nudging my question. I could do with confirmation before proceeding with my current projects. Thank you.
Comment: Extremely small p-values using Limma for proteomic data by Robert Castelo ★ 3.3k
From the point of view of visualization, I find handy the fact that raw p-values give more resolution than adjusted ones, which allows one …
Comment: deseq2 results by ATpoint ★ 4.1k
> the results are not satisfactory to me Well, what is your question? The DESeq2 vignette covers how to do analysis, and some diagnostics…
Comment: Extremely small p-values using Limma for proteomic data by ATpoint ★ 4.1k
It's not an implementation problem I am discussing (it's trivial obviously) -- more that for most purposes the y-axis metric should be the …
Votes
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
Answer: Cannot connect to ExperimentHub server
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Scholar to Robert Castelo ★ 3.3k
Popular Question to Gyan Prakash Mishra ▴ 10
Popular Question to Gordon Smyth 50k
Popular Question to WouterDeCoster ▴ 130
Scholar to Michael Love 42k
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