Showing : DEseq2 • reset
0
votes
4
replies
734
views
How to know what genes are differentially expression in DESeq2 simulation?
deseq2
updated 5.7 years ago by ★ 4.0k • written 5.7 years ago by • 0
0
votes
1
reply
373
views
Choosing DESeq2 design
deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
1
vote
3
replies
1.2k
views
DE analysis outlier removal
deseq2 outlier normalization removal
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
votes
1
reply
861
views
DESeq dispersion parameter
deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
votes
2
replies
1.0k
views
phyloseq_to_deseq2 design strategy for multiple factors analysis (2 or more)
deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
5
votes
2
replies
1.7k
views
DESeq2 pairwise comparisons w/ 3 factors
deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 10
0
votes
6
replies
1.7k
views
Remove batch effect for DESeq2
deseq2
updated 5.7 years ago by 68k • written 5.7 years ago by • 0
0
votes
3
replies
2.1k
views
DESeq2 - cannot find function?
deseq2 r software error
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
4
votes
3
replies
1.2k
views
RNA-Seq analysis with DESeq2: showing two conditions do *not* significantly differ
deseq2 RNA-Seq uniform distribution data visualization
updated 5.7 years ago by ★ 13k • written 5.7 years ago by ▴ 20
0
votes
1
reply
357
views
DESeq2 : Model clarification
deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 20
0
votes
8
replies
3.4k
views
DESeq LRT reduced model
deseq2 LRT
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
votes
5
replies
1.2k
views
Negative Binomial model for microbiome data
deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
1
vote
1
reply
7.1k
views
How to import featureCounts data into DESeq2
DESEq2
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
votes
1
reply
1.4k
views
Adjusting for unwanted variation in DESeq2
DESeq2 deseq2 sva rna-seq differential expression anlaysis
updated 5.7 years ago by 68k • written 5.7 years ago by • 0
1
vote
1
reply
1.1k
views
multifactor desing with interaction LRT or Wald test?
deseq2 LRT wald
updated 5.7 years ago by ★ 4.0k • written 5.7 years ago by ▴ 10
0
votes
1
reply
788
views
Meaning of log2 fold change in 2 x 4 interaction
deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 10
1
vote
3
replies
2.2k
views
In DESeq2, how do you interpret results based on the order of variables in the "contrast" argument?
deseq2
updated 5.7 years ago by ★ 4.0k • written 5.7 years ago by • 0
1
vote
1
reply
564
views
mate pairs read counts as input for DESeq2
deseq2
updated 5.7 years ago by 68k • written 5.7 years ago by ▴ 10
1
vote
2
replies
1.1k
views
Data not getting normalised after DESeq2
deseq2 normalization
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 40
3
votes
6
replies
959
views
MA plot shows inflation of downregulated genes.
deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 10
0
votes
1
reply
3.3k
views
Where in the procedure do I remove low-expressed genes?
deseq2 edger
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
votes
3
replies
1.3k
views
DESeq2 accounting for two confounders with interaction in the design matrix
deseq2 design matrix multi-confounders linear models rna-seq
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
1
vote
3
replies
1.4k
views
DESeq2 - controlling for other variables
deseq2 DEG covariate study design variables
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
1
vote
1
reply
484
views
DESeq2: Identify similarly expressed genes
deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
votes
8
replies
1.4k
views
DESeq2 notice about GLM convergence
deseq2 RNASeq
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
3
votes
3
replies
2.0k
views
Repeated error loading DESqe2 - package xxx not found
deseq2 package software error
updated 5.7 years ago by 25k • written 5.8 years ago by • 0
0
votes
6
replies
2.1k
views
Bizarre Dispersion Plots
deseq2 RNA RNASeq
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
2
votes
2
replies
1.3k
views
RNA-seq analysis with DESeq2
deseq2
updated 5.7 years ago by ▴ 280 • written 5.7 years ago by ▴ 50
2
votes
8
replies
1.5k
views
DESEQ2 design with unequal matching and replicates?
deseq2 RNASeq
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
2
votes
3
replies
728
views
The basis for the full rank design matrix requirement in DESeq2
deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 90
0
votes
2
replies
735
views
DESeq2 error on function results
deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
0
votes
1
reply
1.4k
views
What does an asymmetrical MA plot indicate and how do I know if it means I've made an error?
deseq2 plotMA rnaseq community analysis asymmetry
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
2
votes
3
replies
722
views
Order of levels within factors affects DESeq2 results when interaction is included
deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
1
vote
5
replies
731
views
subtle differences in results based on how Design Table is coded
deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
0
votes
0
replies
922
views
News: RNAseq data analysis with R and Bioconductor
limma deseq2 go edger News
5.8 years ago info ▴ 10
0
votes
3
replies
1.2k
views
how to interpret results from 3way design in DESeq2
deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
0
votes
3
replies
1.6k
views
Highly variable gene analysis including RUVs batch correction
deseq2 RUV batch highly variable genes
updated 5.8 years ago by • 0 • written 5.8 years ago by • 0
4
votes
5
replies
1.7k
views
Difference in dimensionality reduction plots based on DESeq2 R package and core functions for RNA-Seq data
deseq2 vst pca cpm
5.8 years ago svlachavas ▴ 840
2
votes
8
replies
3.4k
views
DESeq2 : log2FC discrepencies between results and lfcShrink
deseq2 shrinkage
updated 3.0 years ago by 43k • written 5.8 years ago by ▴ 20
2
votes
4
replies
1.6k
views
DESeq2 - problem with inferring correct results.
deseq2 rnaseq sva fdrtool ihw
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
0
votes
7
replies
1.7k
views
tximeta doesn't work downloading the ref genome
deseq2 tximeta tximport rnaseq
5.8 years ago rafaelsolersanblas ▴ 50
1
vote
2
replies
1.8k
views
For loop for DESeq2
loop deseq2 rnaseq
updated 3.4 years ago by • 0 • written 5.8 years ago by ▴ 10
0
votes
1
reply
599
views
DESeq2: basemean count
deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 120
0
votes
1
reply
509
views
DESeq2: multiple factors, comparison of a main factor between samples with inconsistent magnitudes of gene expression changes
deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 10
0
votes
1
reply
1.1k
views
DESeq2 with uneven group size
deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
0
votes
1
reply
2.5k
views
RLE plot of DESeq2 normalisation / extract matrix of normalised counts from DESeqDataSet
deseq2 RLE
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
1
vote
3
replies
1.1k
views
DESeq2 : Estimating dispersions takes forever to finish
deseq2
5.8 years ago Nicolas Rosewick ▴ 20
3
votes
5
replies
1.8k
views
Emirical Bayesian shrinkage for dispertion/LFC estimation
rnaseq deseq2
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 10
1
vote
2
replies
581
views
I have four groups in my RNAseq experiment and want to compare them all to each other (not them all to a control). How do I do this is deseq2?
deseq2
updated 5.8 years ago by ★ 1.4k • written 5.8 years ago by • 0
0
votes
2
replies
1.2k
views
DESeq2 Complex Model
deseq2 rnaseq
updated 5.8 years ago by ★ 13k • written 5.8 years ago by ▴ 10
4,839 results • Page 42 of 97
Recent ...
Replies
Comment: upstream git branches of bioc-release by TrentonCollier99 • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments. https://bioc-release.r-univ…
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release by Jeroen ▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Comment: Large logFC but somewhat high FDR by Gordon Smyth 53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Awards • All
Popular Question to efoss ▴ 10
Popular Question to James W. MacDonald 68k
Popular Question to Gordon Smyth 53k
Popular Question to shepherl 4.2k
Popular Question to story.benjamin ▴ 20
Locations • All
United States, just now
United States, 5 minutes ago
United States, 1 hour ago
The city by the bay, 1 hour ago
United States, 2 hours ago
Traffic: 599 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