Showing : DESEQ2 • reset
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 20 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 8 days ago by • 0 • written 4.6 years ago by ▴ 10
3
votes
3
replies
232
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 15 days ago by 42k • written 16 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 9 days ago by ★ 4.1k • written 9 days ago by ▴ 10
3
votes
1
reply
316
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 15 days ago by 42k • written 15 days ago by ▴ 40
2
votes
5
replies
762
views
DESeq2 setting significant p-value
DESeq2
updated 19 days ago by 42k • written 5.0 years ago by ▴ 10
2
votes
9
replies
400
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 13 days ago by 65k • written 13 days ago by • 0
2
votes
3
replies
192
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 3 days ago by ★ 4.1k • written 5 days ago by • 0
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
1
vote
1
reply
127
views
Handling multiple differential expression comparisons
DESeq2
updated 3 days ago by 42k • written 5 days ago by ▴ 10
1
vote
2
replies
200
views
Design Matrix within group comparison more than two groups
DESeq2
26 days ago • updated 25 days ago hemantcnaik • 0
1
vote
2
replies
721
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
21 days ago • updated 12 days ago ussarizona ▴ 10
1
vote
4
replies
485
views
DEseq2 coefficient
DESeq2 coefficient
10 weeks ago • updated 7 days ago JKim • 0
1
vote
1
reply
124
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 8 days ago by 42k • written 8 days ago by • 0
1
vote
3
replies
231
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 12 days ago by 42k • written 13 days ago by • 0
1
vote
4
replies
339
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
14 days ago • updated 12 days ago winwater0928 • 0
1
vote
3
replies
244
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 19 hours ago by ★ 4.1k • written 7 days ago by • 0
1
vote
3
replies
218
views
Different Shrunk Log2FC according with reference
DESeq2
updated 14 days ago by 42k • written 14 days ago by ▴ 20
1
vote
2
replies
245
views
How to retrieve detailed regression results from deseq2
DESeq2
28 days ago • updated 19 days ago Weiqian ▴ 10
0
votes
1
reply
114
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 8 days ago by 42k • written 9 days ago by • 0
0
votes
2
replies
65
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
updated 9 hours ago by ★ 1.3k • written 18 hours ago by • 0
0
votes
2
replies
133
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
8 days ago • updated 5 days ago Aurora • 0
0
votes
1
reply
116
views
putting my own expression data in deseq2
DESeq2
updated 8 days ago by ★ 4.1k • written 8 days ago by • 0
0
votes
2
replies
224
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 29 days ago by 42k • written 4 weeks ago by ▴ 30
0
votes
3
replies
262
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 7 days ago by 42k • written 8 days ago by • 0
0
votes
2
replies
155
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
7 days ago • updated 6 days ago kcarey • 0
0
votes
3
replies
158
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 6 days ago by ★ 4.1k • written 7 days ago by • 0
0
votes
2
replies
215
views
PCA plot suggestions
DESeq2 PCAtools
updated 12 days ago by 42k • written 13 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
4
replies
272
views
DEG with low counts
DESeq2
updated 19 days ago by 42k • written 24 days ago by • 0
0
votes
2
replies
119
views
DESeq2 v1.35.0
DESeq2
updated 6 days ago by 42k • written 6 days ago by • 0
0
votes
7
replies
427
views
DESeq filtering specific to contrasts
DESeq2
updated 19 days ago by 42k • written 11 weeks ago by • 0
0
votes
6
replies
231
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 4 days ago by ★ 1.3k • written 6 days ago by ▴ 130
0
votes
1
reply
135
views
covariate with negative and positive values
DESeq2
updated 20 days ago by 42k • written 22 days ago by • 0
0
votes
1
reply
178
views
DESeq2 gives an error and R crashes
DESeq2
28 days ago • updated 27 days ago Shefali • 0
0
votes
1
reply
153
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 20 days ago by ★ 4.1k • written 21 days ago by • 0
0
votes
4
replies
243
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
21 days ago • updated 18 days ago lonn • 0
0
votes
1
reply
113
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 20 days ago by 42k • written 20 days ago by • 0
0
votes
1
reply
139
views
rlog transformation
DESeq2
updated 20 days ago by 42k • written 20 days ago by • 0
0
votes
2
replies
249
views
Regressing out batch effects
DESeq2
updated 29 days ago by 42k • written 4 weeks ago by • 0
0
votes
4
replies
603
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 22 days ago by 42k • written 6 months ago by • 0
0
votes
8
replies
358
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 13 days ago by ★ 1.3k • written 15 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 14 days ago by 42k • written 14 days ago by • 0
0
votes
1
reply
137
views
Bioinformatics student
Des DESeq2
updated 26 days ago by • 0 • written 26 days ago by • 0
0
votes
3
replies
209
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 22 days ago by 42k • written 23 days ago by ▴ 20
0
votes
1
reply
168
views
IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 29 days ago by 42k • written 29 days ago by • 0
46 results • Page 1 of 1
Recent ...
Replies
Comment: EGSEA usage with microarray data (with vooma)? by Chris • 0
Hi Pekka, I also try EGSEA with microarray data. However, I got this error. Would you please have a suggestion? gsa = egsea.ma(numeric…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
> Any suggestions for methylation data segmentation? I think the same segmentation can be used.
Comment: deseq2 results by swbarnes2 ★ 1.3k
Cross-posted https://www.biostars.org/p/9594331/#9594458
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.
Votes
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
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
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