Showing : DEseq2 • reset
2
votes
5
replies
2.3k
views
DESeq2 on CIRI results ?
deseq2 circrna ciri ciri2
7.6 years ago sbcn ▴ 80
3
votes
7
replies
6.9k
views
Pre-filtering genes counts vs normalised counts DESeq2
deseq2 pre-filtering
updated 7.6 years ago by 43k • written 7.6 years ago by ▴ 40
1
vote
3
replies
1.4k
views
DESEq2: the use of interaction term and grouping with different betaPrior arguments in older version of DESEq2
deseq2 interaction term multiple groups betaprior
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
1
vote
3
replies
1.5k
views
LRT results DESeq2
deseq2 Job
7.6 years ago bekah ▴ 40
0
votes
1
reply
1.1k
views
DESeq2 design for time series data without "untreated"
deseq2 rnaseq multiple time points
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
0
votes
2
replies
853
views
Comparing various genotypes to a control
deseq2
7.6 years ago rattray56 • 0
2
votes
2
replies
8.1k
views
Error in DESeqDataSet(se, design = design, ignoreRank) : all variables in design formula must be columns in colData
deseq2
7.6 years ago yueli7 ▴ 20
2
votes
2
replies
2.4k
views
Deseq2 alternative splicing in understudied organism
deseq2 splicing
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
1
vote
1
reply
1.5k
views
Generating RPKM data from dds (DESeq2 pipeline)
deseq2 dds RPKM
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
0
votes
5
replies
1.7k
views
DEseq2 differentially expressed genes have lower expression values than non-differentially expressed genes
deseq2 R
7.6 years ago lychen83 • 0
1
vote
8
replies
5.1k
views
DESeq2: betaPrior changes significance dramatically
deseq2 betaPrior shrinkage significance
7.6 years ago brynedal ▴ 40
0
votes
13
replies
2.2k
views
Artificial P-value caused by outlier samples
deseq2
written 7.6 years ago by ▴ 10
2
votes
5
replies
1.4k
views
trouble in install DESeq2
deseq2 package installation
7.6 years ago yueli7 ▴ 20
0
votes
8
replies
2.8k
views
inter-species RNA-seq with DEseq2: how to account for gene length differences
deseq2 normalization
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
0
votes
1
reply
1.0k
views
DESeq2: Multifactor design working with example data but not with my data
deseq2 multiple factor design
updated 7.6 years ago by 43k • written 7.6 years ago by ▴ 10
1
vote
2
replies
1.6k
views
Study design in DESeq2
deseq2 Model matrix not full rank model.matrix study design
7.6 years ago Krzysztof Kolmus ▴ 10
4
votes
3
replies
1.6k
views
DESeq2 why estimate dispersion on log scale
deseq2 dispersoin estimatedispersions
written 7.6 years ago by • 0
0
votes
3
replies
1.5k
views
Analyzing a subgroups of samples, which result should I trust
deseq2 rna-seq
written 7.6 years ago by ▴ 20
1
vote
1
reply
1.2k
views
Post-processing RNA-Seq after tximport
salmon rna seq tximport ruv-seq deseq2
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
1
vote
5
replies
2.0k
views
p-value the same for different contrasts DESeq2
deseq2 design and contrast matrix
updated 9 months ago by ▴ 10 • written 7.6 years ago by ▴ 10
1
vote
2
replies
546
views
OTU versus Sequence in Test Results Table
deseq2
7.6 years ago irene.yang ▴ 10
0
votes
1
reply
939
views
Identifying ago2 enriched genes under 2 different conditions
DESeq2 RIP
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
1
vote
2
replies
4.2k
views
dyld: Library not loaded: @rpath/libc++abi.1.dylib
DESeq2 biocLite
updated 7.6 years ago by ★ 6.6k • written 7.6 years ago by • 0
1
vote
5
replies
1.7k
views
Comparing RNA-Seq expression data from different sequencers (HiSeq3000 and NovaSeq6000) - are there methods for batch effect corrections?
deseq2 rna-seq illumina batch effect
updated 7.6 years ago by 43k • written 7.6 years ago by ▴ 40
0
votes
1
reply
997
views
RNAseq DESeq2 paired data design help
rnaseq design matrix deseq2
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
0
votes
3
replies
1.6k
views
Group comparison using DESeq
deseq2 multiple groups
updated 7.6 years ago by 68k • written 7.6 years ago by • 0
32
votes
16
replies
21k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport deseq2 TPM RPKM rnaseq
updated 7.6 years ago by ▴ 20 • written 9.4 years ago by ▴ 200
0
votes
1
reply
814
views
How to use normalized DESeq2 data for downstream analysis?
deseq2 normalization
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
3
votes
1
reply
26k
views
DESEQ2, VST PCA/Clustering: Is it not advisable to standard normalize data?
deseq2
updated 7.6 years ago by 43k • written 7.6 years ago by ▴ 10
1
vote
3
replies
1.7k
views
Information regarding the (minimum) number of genes needed to analyse with DESeq2
deseq2
7.6 years ago suranandbabu85 • 0
1
vote
3
replies
943
views
Differentially expressed genes detection between three classes with a batch effect in DESeq2
deseq2 batch effect differential gene expression
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
1
vote
3
replies
1.6k
views
Results counts post DESeq same raw counts
DESeq2 results
updated 7.6 years ago by 43k • written 7.6 years ago by ▴ 60
2
votes
4
replies
2.4k
views
DESeq2 with multi level
deseq2 lfcshrink
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
1
vote
2
replies
2.4k
views
DESEq2 Principal Component Analysis with different genes biotypes (protein coding, miRNAs, lncRNAs, etc)
DESeq2 PCA rlog transformation biotype
7.6 years ago JoannaF ▴ 10
1
vote
2
replies
9.4k
views
DESEQ2 design with multiple conditions
deseq2 design matrix
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
0
votes
3
replies
1.2k
views
interaction model deseq2 specific DE genes
deseq2 interaction model differential expression
updated 7.6 years ago by 43k • written 7.6 years ago by ▴ 90
1
vote
8
replies
1.5k
views
Unexpected differences in results from paired analysis with DESeq2
DESEq2 paired analysis factor levels
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
0
votes
1
reply
1.1k
views
DESeq2 - Test for linear combinations
deseq2 linear combination
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
4
votes
6
replies
9.8k
views
DESeq2 Error in varianceStabilizingTransformation
deseq2
updated 7.6 years ago by • 0 • written 11.1 years ago by ▴ 10
1
vote
1
reply
586
views
miRNA DE analysis using DeSeq2
deseq2
updated 7.6 years ago by 43k • written 7.6 years ago by ▴ 10
2
votes
3
replies
1.1k
views
Understand how DESeq estimates SE for log2 fold change
deseq2
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
1
vote
10
replies
1.8k
views
Allele-specific expression with different gene lenghts
deseq2 allele-specific-expression rnaseq
updated 7.6 years ago by 43k • written 7.6 years ago by ▴ 10
0
votes
13
replies
7.9k
views
DESeq2: Poor dispersion fit, even when a local or custom fit is used
deseq2 dispersion
7.6 years ago Frederik Ziebell ▴ 30
0
votes
2
replies
871
views
normalisation of count data
deseq2
updated 7.6 years ago by ★ 7.9k • written 7.6 years ago by • 0
0
votes
2
replies
1.4k
views
DESeq account for using two different siRNA constructs to knockdown same gene
deseq2 design and contrast matrix multiple factor design design matrix
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
0
votes
4
replies
1.9k
views
colData and design problem
deseq2
7.6 years ago soheilazareie • 0
0
votes
2
replies
1.4k
views
tech replicates or bio replicate?
deseq2
updated 7.6 years ago by • 0 • written 7.7 years ago by ▴ 10
0
votes
1
reply
613
views
DESeq2 (Different results when using interactive term equation)
DESeq2
updated 7.6 years ago by 43k • written 7.6 years ago by ▴ 10
4
votes
8
replies
8.0k
views
Convert Normalized RNA-Seq counts to TPM after Batch Correction
sva deseq2 limma
updated 3.3 years ago by • 0 • written 7.7 years ago by ▴ 70
1
vote
2
replies
1.6k
views
deseq2 normalization with metagenomics data
deseq2
updated 7.7 years ago by ★ 1.1k • written 7.7 years ago by ▴ 860
4,840 results • Page 64 of 97
Recent ...
Replies
Comment: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
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.
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 shepherl 4.2k
Popular Question to Gordon Smyth 53k
Popular Question to k___ ▴ 30
Popular Question to efoss ▴ 10
Popular Question to James W. MacDonald 68k
Locations • All
United States, 26 minutes ago
The city by the bay, 29 minutes ago
United States, 35 minutes ago
United States, 1 hour ago
United States, 1 hour ago
Traffic: 1129 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