Showing : DEseq2 • reset
0
votes
1
reply
1.7k
views
DeSeq2 normalization 16S
DESeq2
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
0
votes
4
replies
1.5k
views
DESeq2 : standardising variation between treatments
RNA-seq DESeq2
2.1 years ago ar14g12 • 0
0
votes
2
replies
860
views
Issues with ddseq2 for treatment response factoring in different KO clones
Clonality RNASeq DESeq2
updated 2.1 years ago by ★ 1.4k • written 2.1 years ago by • 0
0
votes
1
reply
912
views
DeSeq2 data comparison and extracting outputs
DESeq2
updated 2.1 years ago by ★ 1.4k • written 2.1 years ago by • 0
1
vote
5
replies
1.6k
views
Mixed up sample info with plotPCA
plotMA ggplot2 plotPCA DESeq2
updated 2.1 years ago by 43k • written 2.2 years ago by • 0
0
votes
4
replies
1.1k
views
Extract LRT results for each comparison
LRT DESeq2
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
2
votes
4
replies
1.6k
views
Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
2.2 years ago Shihui • 0
0
votes
5
replies
1.1k
views
DESeq2, results(dds, name = <reference>) interpretation results
DESeq2
2.2 years ago Rockbar • 0
0
votes
3
replies
1.0k
views
Deseq2, multifactor model design for comparing adult Mutant mouse versus pup Mutant mouse with normalization to the age difference of the Wildtype co…
DGE DESeq2
2.2 years ago ruba-mahmoud • 0
0
votes
5
replies
1.2k
views
DeSeq2 design fails (full model matrix is less than full rank)
DESeq2
updated 2.2 years ago by 68k • written 2.2 years ago by ▴ 10
1
vote
3
replies
2.5k
views
How does DESeq2 calculate FPKM values when gene lengths are not supplied?
deseq2
written 5.7 years ago by • 0
0
votes
4
replies
1.5k
views
filtering out lowly expressed genes by groups
RNASeqData DESeq2
updated 2.2 years ago by 68k • written 2.2 years ago by ▴ 10
1
vote
3
replies
1.5k
views
Deseq2, enrichGO and ensembl ID
go DESeq2
updated 10 months ago by 68k • written 2.2 years ago by • 0
0
votes
3
replies
894
views
how to adjust other conditions when calling DEGs by DESeq2
DifferentialExpression DESeq2
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
0
votes
3
replies
980
views
The meaning of the analysis results when using a new metric in analysis
DESeq2
updated 2.2 years ago by 68k • written 2.2 years ago by ▴ 10
1
vote
1
reply
1.6k
views
Can I transform already normalized rna-seq data with Z-score?
Z-score RNASeqData Deseq DESeq2
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
0
votes
1
reply
850
views
How to compared two groups out of twelve in DESeq2
DESeq2
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
1
vote
7
replies
1.9k
views
Permutation test in DESeq2?
DESeq2
updated 2.2 years ago by 43k • written 2.2 years ago by • 0
3
votes
3
replies
1.1k
views
EdgeR and DESeq2, variance estimation and parametric test
parametrictest edgeR DESeq2
2.2 years ago Nisha • 0
3
votes
5
replies
2.2k
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
0
votes
1
reply
590
views
Run DESeq2 on chromosome and plasmids separately
DESeq2
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by ▴ 10
0
votes
1
reply
686
views
Unable to create ddf object
DESeqDataSetFromMatrix dds DESeq2
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
0
votes
2
replies
1.0k
views
RSubread DESeq2
RNASeqData DifferentialExpression DESeq2
2.2 years ago Beyza • 0
0
votes
3
replies
948
views
Dramatically different DESeq2 results in Mac and Linux computers
DESeq2
updated 2.2 years ago by 68k • written 2.2 years ago by ▴ 30
1
vote
2
replies
741
views
Setting up a multi-factor experiement
DESeq2
2.2 years ago • updated 2.1 years ago jon50250 • 0
0
votes
1
reply
851
views
DESeq design and contrast with multiple factors
RNASeq DESeq2
updated 2.2 years ago by 43k • written 2.2 years ago by • 0
1
vote
1
reply
1.2k
views
results after deseq2 not showing gene ids and gene names but they are present in dds object
DESeq2
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
0
votes
3
replies
1.5k
views
DESeq2 not full rank with paired patient samples and one control cohort
DESeq2
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
0
votes
3
replies
1.4k
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 2.2 years ago by ★ 1.9k • written 2.2 years ago by • 0
0
votes
1
reply
848
views
Is it possible to combine count gene expression data coming from one sequencing technology (RNA seq) with intensity gene expression data coming from …
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
0
votes
1
reply
1.2k
views
How to properly compare the group-specific samples using DEseq2
DESeq2
updated 2.2 years ago by ★ 1.4k • written 2.2 years ago by • 0
5
votes
13
replies
4.3k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 2.2 years ago by 43k • written 2.2 years ago by • 0
0
votes
5
replies
1.6k
views
How to use contrast with multiple treatments?
RNASeqdataanalysis DESeq2
updated 2.2 years ago by ★ 1.4k • written 2.2 years ago by • 0
2
votes
2
replies
1.6k
views
DESeq2 results - Annotating and exporting results
DESeq2
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
3
votes
7
replies
1.7k
views
DESeq2 alternative hypyothesis: testing for genes NOT significantly downregulated
DESeq2
2.3 years ago casco ▴ 10
0
votes
9
replies
1.7k
views
DESeq2: How to estimate effects of one factor controlling for other factors?
DESeq2
2.3 years ago • updated 2.2 years ago mjd275 • 0
1
vote
8
replies
4.3k
views
Significantly regulated genes produced by only a few affected samples
deseq2
written 7.7 years ago by ▴ 60
2
votes
12
replies
2.9k
views
P-value inflation?
DESeq2
updated 2.2 years ago by 68k • written 2.3 years ago by ▴ 10
1
vote
2
replies
1.4k
views
DESeq2 batch design
DESeq2
updated 2.3 years ago by ★ 1.4k • written 2.3 years ago by ▴ 10
0
votes
1
reply
1.1k
views
Getting NAs in both p-values (normal and adjusted) in DEseq2
DESeq2
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
8
votes
15
replies
3.3k
views
PCA percent variance DESeq2
PCA DESeq2
2.3 years ago • updated 2.2 years ago IUH • 0
1
vote
6
replies
3.5k
views
Time-series RNA-seq analysis using DESeq2
time-series DESeq2 RNASeq timecoursedata TimeCourse
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
0
votes
1
reply
926
views
Comparing the effect of single drug and two-drug combination with control in RNA seq data
GeneExpressionWorkflow DESeq2
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
0
votes
1
reply
634
views
DEG by deseq2 by Race
DESeq2
updated 2.3 years ago by ★ 4.0k • written 2.3 years ago by • 0
0
votes
1
reply
739
views
the confuse issue in DEseq2 among multi group
DESeq2
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
3
votes
2
replies
2.8k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG DESeq2 biomaRt clusterProfiler org.Mm.eg.db
updated 2.3 years ago by ★ 4.1k • written 2.3 years ago by ▴ 10
5
votes
2
replies
1.8k
views
can't install DESeq2 ("unable to access index for repository")
biocmanager DESeq2
2.3 years ago Alessia ▴ 40
2
votes
5
replies
2.8k
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2 BatchEffect limma
updated 2.3 years ago by 53k • written 2.3 years ago by • 0
0
votes
1
reply
860
views
FALSE error when checking a pre made sample data
Rstudio scRNAseq DESeq2
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
0
votes
2
replies
724
views
No such file or directory DESeq2
rstudioScRNA DESeq2
written 2.3 years ago by • 0
4,839 results • Page 10 of 97
Recent ...
Replies
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"]) ```
Answer: p.adjust BH Question by Gordon Smyth 53k
Duplicate of https://support.bioconductor.org/p/41077/
Answer: Large logFC but somewhat high FDR by Gordon Smyth 53k
Glad you're getting good use out of the package. The results that you show seem pretty much as one would expect, with nothing surprising. …
Votes
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
A: p.adjust BH generates duplicate values
Awards • All
Popular Question to shepherl 4.2k
Popular Question to story.benjamin ▴ 20
Popular Question to Gordon Smyth 53k
Supporter to fabio.marroni • 0
Popular Question to Guido Hooiveld ★ 4.1k
Locations • All
United States, 58 minutes ago
Switzerland, 1 hour ago
United States, 1 hour ago
India, 1 hour ago
Brazil, 1 hour ago
Traffic: 779 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