Showing : deseq2 • reset
2
votes
2
replies
91
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 11 hours ago by 41k • written 11 hours ago by • 0
0
votes
0
replies
26
views
Handling multiple differential expression comparisons
DESeq2
12 hours ago Zainab • 0
0
votes
6
replies
135
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 41 minutes ago by ★ 1.3k • written 1 day ago by ▴ 130
0
votes
2
replies
72
views
DESeq2 v1.35.0
DESeq2
updated 1 day ago by 41k • written 1 day ago by • 0
0
votes
2
replies
105
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
2 days ago • updated 1 day ago kcarey • 0
0
votes
3
replies
110
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 1 day ago by ★ 4.1k • written 2 days ago by • 0
0
votes
1
reply
115
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 2 days ago by ★ 4.1k • written 2 days ago by • 0
0
votes
3
replies
230
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 2 days ago by 41k • written 3 days ago by • 0
1
vote
1
reply
93
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 3 days ago by 41k • written 3 days ago by • 0
0
votes
1
reply
93
views
putting my own expression data in deseq2
DESeq2
updated 3 days ago by ★ 4.1k • written 3 days ago by • 0
0
votes
2
replies
105
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
3 days ago • updated 21 hours ago Aurora • 0
0
votes
1
reply
91
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 3 days ago by 41k • written 4 days ago by • 0
3
votes
3
replies
205
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 4 days ago by ★ 4.1k • written 5 days ago by ▴ 10
1
vote
3
replies
199
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 7 days ago by 41k • written 8 days ago by • 0
2
votes
9
replies
356
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 8 days ago by 65k • written 8 days ago by • 0
0
votes
2
replies
190
views
PCA plot suggestions
DESeq2 PCAtools
updated 7 days ago by 41k • written 9 days ago by • 0
0
votes
1
reply
141
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 9 days ago by 41k • written 9 days ago by • 0
1
vote
3
replies
205
views
Different Shrunk Log2FC according with reference
DESeq2
updated 9 days ago by 41k • written 9 days ago by ▴ 20
1
vote
4
replies
310
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
9 days ago • updated 8 days ago winwater0928 • 0
3
votes
1
reply
302
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 10 days ago by 41k • written 10 days ago by ▴ 40
0
votes
8
replies
335
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 9 days ago by ★ 1.3k • written 10 days ago by • 0
3
votes
3
replies
219
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 10 days ago by 41k • written 11 days ago by • 0
0
votes
1
reply
132
views
rlog transformation
DESeq2
updated 15 days ago by 41k • written 15 days ago by • 0
0
votes
1
reply
109
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 15 days ago by 41k • written 15 days ago by • 0
0
votes
4
replies
233
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
16 days ago • updated 14 days ago lonn • 0
1
vote
2
replies
699
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
16 days ago • updated 7 days ago ussarizona ▴ 10
0
votes
1
reply
141
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 15 days ago by ★ 4.1k • written 16 days ago by • 0
0
votes
1
reply
130
views
covariate with negative and positive values
DESeq2
updated 15 days ago by 41k • written 17 days ago by • 0
0
votes
3
replies
203
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 17 days ago by 41k • written 18 days ago by ▴ 20
0
votes
4
replies
261
views
DEG with low counts
DESeq2
updated 14 days ago by 41k • written 19 days ago by • 0
0
votes
1
reply
130
views
Deseq2 Rlog transformation
DESeq2
updated 18 days ago by ★ 4.1k • written 20 days ago by • 0
1
vote
2
replies
191
views
Design Matrix within group comparison more than two groups
DESeq2
21 days ago • updated 20 days ago hemantcnaik • 0
0
votes
1
reply
131
views
Bioinformatics student
Des DESeq2
updated 21 days ago by • 0 • written 21 days ago by • 0
0
votes
1
reply
174
views
DESeq2 gives an error and R crashes
DESeq2
23 days ago • updated 22 days ago Shefali • 0
1
vote
2
replies
239
views
How to retrieve detailed regression results from deseq2
DESeq2
23 days ago • updated 14 days ago Weiqian ▴ 10
0
votes
1
reply
160
views
IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 24 days ago by 41k • written 24 days ago by • 0
0
votes
2
replies
164
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 28 days ago by 65k • written 28 days ago by • 0
0
votes
2
replies
216
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 24 days ago by 41k • written 28 days ago by ▴ 30
0
votes
2
replies
238
views
Regressing out batch effects
DESeq2
updated 24 days ago by 41k • written 29 days ago by • 0
1
vote
1
reply
163
views
DESeq2 - Missing values in count matrix
DESeq2
updated 29 days ago by 65k • written 29 days ago by • 0
1
vote
6
replies
429
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 4 weeks ago by 41k • written 4 weeks ago by • 0
1
vote
1
reply
152
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
4 weeks ago Layal • 0
0
votes
2
replies
171
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
4 weeks ago michelafrancesconi8 • 0
0
votes
4
replies
256
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 4 weeks ago by 41k • written 4 weeks ago by • 0
0
votes
1
reply
160
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 5 weeks ago by 41k • written 5 weeks ago by • 0
2
votes
3
replies
347
views
PCA of different bacterial species
DESeq2
updated 5 weeks ago by 41k • written 5 weeks ago by ▴ 10
3
votes
2
replies
213
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
5 weeks ago Anita ▴ 10
0
votes
1
reply
169
views
collapseReplicates dimension error
DESeq2 Dese
updated 5 weeks ago by 41k • written 6 weeks ago by • 0
1
vote
2
replies
231
views
DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
6 weeks ago • updated 5 weeks ago Chanderkant Chaudhary • 0
0
votes
2
replies
226
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
6 weeks ago kcarey • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
Awards • All
Popular Question to Gordon Smyth 50k
Popular Question to Zainab • 0
Popular Question to Theo ▴ 10
Popular Question to gene_bioconductor ▴ 10
Popular Question to rohitsatyam102 ▴ 20
Locations • All
France, 12 minutes ago
Iran, 35 minutes ago
San Diego, 41 minutes ago
The city by the bay, 43 minutes ago
WEHI, Melbourne, Australia, 2 hours ago
Traffic: 405 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