Showing : DESeq2 • reset
0
votes
2
replies
64
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
updated 9 hours ago by ★ 1.3k • written 18 hours 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
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
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
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
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
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 18 hours ago by ★ 4.1k • written 7 days ago by • 0
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
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
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
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
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
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
0
votes
2
replies
215
views
PCA plot suggestions
DESeq2 PCAtools
updated 12 days ago by 42k • written 13 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
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
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
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
4
replies
339
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 15 days ago by 42k • written 15 days ago by ▴ 40
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
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
0
votes
1
reply
139
views
rlog transformation
DESeq2
updated 20 days ago by 42k • written 20 days ago by • 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
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
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
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
3
replies
209
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 22 days ago by 42k • written 23 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
4
replies
272
views
DEG with low counts
DESeq2
updated 19 days ago by 42k • written 24 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
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
0
votes
1
reply
137
views
Bioinformatics student
Des DESeq2
updated 26 days ago by • 0 • written 26 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
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
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
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
2
replies
173
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 4 weeks ago by 65k • written 4 weeks ago by • 0
1
vote
1
reply
170
views
DESeq2 - Missing values in count matrix
DESeq2
updated 4 weeks ago by 65k • written 4 weeks ago by • 0
1
vote
6
replies
441
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 5 weeks ago by 42k • written 5 weeks ago by • 0
1
vote
1
reply
158
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
5 weeks ago Layal • 0
0
votes
2
replies
175
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
5 weeks ago michelafrancesconi8 • 0
0
votes
4
replies
268
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 5 weeks ago by 42k • written 5 weeks ago by • 0
0
votes
1
reply
168
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 5 weeks ago by 42k • written 5 weeks ago by • 0
2
votes
3
replies
360
views
PCA of different bacterial species
DESeq2
updated 6 weeks ago by 42k • written 6 weeks ago by ▴ 10
0
votes
1
reply
172
views
collapseReplicates dimension error
DESeq2 Dese
updated 6 weeks ago by 42k • written 6 weeks ago by • 0
3
votes
2
replies
220
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
6 weeks ago Anita ▴ 10
1
vote
2
replies
239
views
DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
6 weeks ago Chanderkant Chaudhary • 0
50 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
Awards • All
Teacher to Michael Love 42k
Popular Question to Haibo Liu • 0
Popular Question to HS ▴ 10
Popular Question to DevelopingHippo • 0
Scholar to Robert Castelo ★ 3.3k
Locations • All
South Korea, 1 minute ago
India, 6 minutes ago
The city by the bay, 27 minutes ago
WEHI, Melbourne, Australia, 28 minutes ago
Australia, 30 minutes ago
Traffic: 457 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