Showing : DESEq2 • reset
0
votes
1
reply
18
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
43 minutes ago • updated 39 minutes ago Alexandre • 0
0
votes
0
replies
22
views
PCA plot suggestions
DESeq2 PCAtools
9 hours ago Aaliya • 0
0
votes
1
reply
70
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 16 hours ago by 41k • written 19 hours ago by • 0
1
vote
3
replies
84
views
Different Shrunk Log2FC according with reference
DESeq2
updated 1 day ago by 41k • written 1 day ago by ▴ 20
0
votes
3
replies
92
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
updated just now by 65k • written 1 day ago by • 0
2
votes
1
reply
163
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 1 day ago by 41k • written 1 day ago by ▴ 40
0
votes
8
replies
212
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 7 hours ago by ★ 1.3k • written 1 day ago by • 0
3
votes
3
replies
155
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 1 day ago by 41k • written 2 days ago by • 0
0
votes
1
reply
88
views
rlog transformation
DESeq2
updated 6 days ago by 41k • written 7 days ago by • 0
0
votes
1
reply
86
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 6 days ago by 41k • written 7 days ago by • 0
0
votes
1
reply
96
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 6 days ago by 41k • written 7 days ago by • 0
0
votes
1
reply
113
views
covariate with negative and positive values
DESeq2
updated 6 days ago by 41k • written 8 days ago by • 0
0
votes
1
reply
113
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 7 days ago by ★ 4.0k • written 8 days ago by • 0
0
votes
4
replies
194
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
7 days ago • updated 5 days ago lonn • 0
0
votes
3
replies
174
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 8 days ago by 41k • written 9 days ago by ▴ 20
1
vote
2
replies
218
views
How to retrieve detailed regression results from deseq2
DESeq2
14 days ago • updated 5 days ago Weiqian ▴ 10
0
votes
4
replies
229
views
DEG with low counts
DESeq2
updated 6 days ago by 41k • written 10 days ago by • 0
0
votes
1
reply
109
views
Deseq2 Rlog transformation
DESeq2
updated 10 days ago by ★ 4.0k • written 11 days ago by • 0
1
vote
2
replies
163
views
Design Matrix within group comparison more than two groups
DESeq2
12 days ago hemantcnaik • 0
0
votes
1
reply
117
views
Bioinformatics student
Des DESeq2
updated 12 days ago by • 0 • written 12 days ago by • 0
0
votes
1
reply
155
views
DESeq2 gives an error and R crashes
DESeq2
14 days ago • updated 13 days ago Shefali • 0
0
votes
2
replies
192
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 15 days ago by 41k • written 20 days ago by ▴ 30
0
votes
1
reply
141
views
IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 15 days ago by 41k • written 15 days ago by • 0
0
votes
2
replies
220
views
Regressing out batch effects
DESeq2
updated 15 days ago by 41k • written 20 days ago by • 0
0
votes
2
replies
142
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 19 days ago by 65k • written 19 days ago by • 0
1
vote
1
reply
152
views
DESeq2 - Missing values in count matrix
DESeq2
updated 20 days ago by 65k • written 20 days ago by • 0
1
vote
6
replies
402
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 21 days ago by 41k • written 21 days ago by • 0
1
vote
1
reply
136
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
22 days ago Layal • 0
0
votes
2
replies
152
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
22 days ago michelafrancesconi8 • 0
0
votes
4
replies
229
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 22 days ago by 41k • written 23 days ago by • 0
0
votes
1
reply
142
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 27 days ago by 41k • written 27 days ago by • 0
2
votes
3
replies
324
views
PCA of different bacterial species
DESeq2
updated 29 days ago by 41k • written 29 days ago by ▴ 10
0
votes
1
reply
158
views
collapseReplicates dimension error
DESeq2 Dese
updated 4 weeks ago by 41k • written 4 weeks ago by • 0
3
votes
2
replies
200
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
4 weeks ago Anita ▴ 10
1
vote
2
replies
212
views
DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
4 weeks ago • updated 28 days ago Chanderkant Chaudhary • 0
0
votes
2
replies
210
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
5 weeks ago • updated 4 weeks ago kcarey • 0
2
votes
3
replies
285
views
DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 5 weeks ago by 41k • written 5 weeks ago by ▴ 20
0
votes
3
replies
243
views
Help with Complex DESeq2 Design
DESeq2
updated 5 weeks ago by ★ 4.0k • written 5 weeks ago by • 0
1
vote
1
reply
164
views
Need help with creating and plotting temporal clustering analysis of DEGs
DESeq2 ctsGE
updated 5 weeks ago by 41k • written 5 weeks ago by • 0
0
votes
1
reply
132
views
Help with DESeqDataSetFromHTSeqCount
DESeq2 RSeqAn
updated 5 weeks ago by 41k • written 5 weeks ago by • 0
0
votes
1
reply
164
views
lfcShrink error: the line search routine failed
apeglm DESeq2
updated 5 weeks ago by 41k • written 5 weeks ago by • 0
2
votes
2
replies
207
views
With DESeq2 "Not full rank" Error with design
DESeq2 DEs
5 weeks ago feather-W • 0
0
votes
2
replies
302
views
Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 6 weeks ago by 41k • written 6 weeks ago by • 0
0
votes
4
replies
405
views
DESeq2: subtract effect of an isotope control before comparing to a baseline sample?
DESeq2
updated 5 weeks ago by 41k • written 6 weeks ago by • 0
0
votes
7
replies
407
views
DESeq2 filtering vs edgeR filtering
DESeq2
6 weeks ago • updated 29 days ago fr8712ca-s • 0
0
votes
2
replies
239
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
6 weeks ago • updated 5 weeks ago kcarey • 0
1
vote
1
reply
206
views
i'm not getting any differentially expressed genes.
DESeq2
updated 6 weeks ago by ★ 4.0k • written 6 weeks ago by • 0
2
votes
1
reply
233
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 6 weeks ago by ★ 4.0k • written 6 weeks ago by • 0
1
vote
1
reply
195
views
Perform PCA for sample clustering using DESeq2
DESeq2
updated 6 weeks ago by ★ 4.0k • written 6 weeks ago by • 0
0
votes
3
replies
359
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 11 weeks ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…
Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Awards • All
Scholar to James W. MacDonald 65k
Supporter to JKim • 0
Popular Question to Gordon Smyth 50k
Popular Question to Chris • 0
Supporter to Jonathan ▴ 10
Locations • All
United States, just now
EMBL Heidelberg, 3 minutes ago
France, 3 minutes ago
Germany, 9 minutes ago
Belgium, 15 minutes ago
Traffic: 992 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