Showing : deseq2 • reset
0
votes
1
reply
558
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 18 months ago by 43k • written 18 months ago by • 0
0
votes
1
reply
442
views
putting my own expression data in deseq2
DESeq2
updated 18 months ago by ★ 5.0k • written 18 months ago by • 0
3
votes
3
replies
1.1k
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 18 months ago by ★ 5.0k • written 18 months ago by ▴ 10
0
votes
2
replies
706
views
PCA plot suggestions
DESeq2 PCAtools
updated 18 months ago by 43k • written 18 months ago by • 0
1
vote
3
replies
1.0k
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 18 months ago by 43k • written 18 months ago by • 0
2
votes
9
replies
1.7k
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 18 months ago by 68k • written 18 months ago by • 0
0
votes
1
reply
826
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 18 months ago by 43k • written 18 months ago by • 0
1
vote
3
replies
731
views
Different Shrunk Log2FC according with reference
DESeq2
updated 18 months ago by 43k • written 18 months ago by ▴ 20
1
vote
4
replies
1.0k
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
18 months ago winwater0928 • 0
3
votes
1
reply
852
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 18 months ago by 43k • written 18 months ago by ▴ 40
0
votes
7
replies
2.6k
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 18 months ago by ★ 1.4k • written 18 months ago by • 0
3
votes
3
replies
1.1k
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 18 months ago by 43k • written 18 months ago by • 0
0
votes
1
reply
445
views
rlog transformation
DESeq2
updated 18 months ago by 43k • written 18 months ago by • 0
0
votes
1
reply
1.2k
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 18 months ago by 43k • written 18 months ago by • 0
1
vote
2
replies
3.3k
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
18 months ago Patadù ▴ 20
0
votes
1
reply
422
views
covariate with negative and positive values
DESeq2
updated 18 months ago by 43k • written 18 months ago by • 0
0
votes
1
reply
426
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 18 months ago by ★ 5.0k • written 18 months ago by • 0
0
votes
4
replies
921
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
18 months ago lonn • 0
0
votes
3
replies
709
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 18 months ago by 43k • written 18 months ago by ▴ 20
1
vote
2
replies
916
views
How to retrieve detailed regression results from deseq2
DESeq2
18 months ago Weiqian ▴ 10
0
votes
4
replies
925
views
DEG with low counts
DESeq2
updated 18 months ago by 43k • written 18 months ago by • 0
0
votes
1
reply
394
views
Deseq2 Rlog transformation
DESeq2
updated 18 months ago by ★ 5.0k • written 18 months ago by • 0
1
vote
2
replies
762
views
Design Matrix within group comparison more than two groups
DESeq2
18 months ago hemantcnaik • 0
0
votes
1
reply
516
views
Bioinformatics student
Des DESeq2
updated 18 months ago by • 0 • written 18 months ago by • 0
0
votes
1
reply
736
views
DESeq2 gives an error and R crashes
DESeq2
18 months ago Shefali • 0
0
votes
2
replies
793
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 18 months ago by 43k • written 18 months ago by ▴ 70
0
votes
1
reply
812
views
IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 18 months ago by 43k • written 18 months ago by • 0
0
votes
2
replies
730
views
Regressing out batch effects
DESeq2
updated 18 months ago by 43k • written 18 months ago by • 0
0
votes
2
replies
975
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 18 months ago by 68k • written 18 months ago by • 0
1
vote
1
reply
801
views
DESeq2 - Missing values in count matrix
DESeq2
updated 18 months ago by 68k • written 18 months ago by • 0
1
vote
6
replies
1.6k
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 19 months ago by 43k • written 19 months ago by • 0
1
vote
1
reply
487
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
19 months ago Layal • 0
0
votes
2
replies
698
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
19 months ago michelafrancesconi8 • 0
0
votes
4
replies
1.0k
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 19 months ago by 43k • written 19 months ago by • 0
0
votes
1
reply
431
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 19 months ago by 43k • written 19 months ago by • 0
2
votes
4
replies
1.3k
views
PCA of different bacterial species
DESeq2
written 19 months ago by ▴ 10
0
votes
1
reply
578
views
collapseReplicates dimension error
DESeq2 Dese
updated 19 months ago by 43k • written 19 months ago by • 0
3
votes
2
replies
739
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
19 months ago Anita ▴ 10
1
vote
2
replies
844
views
DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
19 months ago Chanderkant Chaudhary • 0
0
votes
2
replies
1.9k
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
19 months ago kcarey • 0
2
votes
3
replies
788
views
DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 19 months ago by 43k • written 19 months ago by ▴ 20
0
votes
3
replies
903
views
Help with Complex DESeq2 Design
DESeq2
updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
1
vote
1
reply
684
views
Need help with creating and plotting temporal clustering analysis of DEGs
DESeq2 ctsGE
updated 19 months ago by 43k • written 19 months ago by • 0
0
votes
1
reply
430
views
Help with DESeqDataSetFromHTSeqCount
DESeq2 RSeqAn
updated 19 months ago by 43k • written 19 months ago by • 0
0
votes
1
reply
1.5k
views
lfcShrink error: the line search routine failed
apeglm DESeq2
updated 19 months ago by 43k • written 19 months ago by • 0
2
votes
2
replies
742
views
With DESeq2 "Not full rank" Error with design
DESeq2 DEs
19 months ago feather-W • 0
0
votes
2
replies
1.1k
views
Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 19 months ago by 43k • written 19 months ago by • 0
0
votes
4
replies
856
views
DESeq2: subtract effect of an isotope control before comparing to a baseline sample?
DESeq2
updated 19 months ago by 43k • written 19 months ago by • 0
0
votes
10
replies
1.6k
views
DESeq2 filtering vs edgeR filtering
DESeq2
written 19 months ago by • 0
0
votes
2
replies
3.0k
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
19 months ago kcarey • 0
4,835 results • Page 6 of 97
Recent ...
Replies
Answer: Using DESeq2 for age prediction by ATpoint ★ 5.0k
The package has no such inbuilt function but you are free to use the vst (or any normalized) counts to train a regression model or classifi…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis by Michael Love 43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Votes
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
Awards • All
Popular Question to Gordon Smyth 53k
Popular Question to Matej • 0
Popular Question to Hervé Pagès 16k
Popular Question to Josef Frank • 0
Popular Question to dan.gatti • 0
Locations • All
United States, 1 minute ago
United States, 21 minutes ago
Germany, 38 minutes ago
United States, 42 minutes ago
The city by the bay, 46 minutes ago
Traffic: 781 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