Showing : DeSeq2 • reset
4
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1.9k
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Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
DESeq2 idep RNASeqData
updated 3.8 years ago by ★ 1.4k • written 3.8 years ago by ▴ 10
0
votes
5
replies
7.4k
views
DESeq2/Differential expression analysis without replicates
DESeq2 DEG
updated 3.2 years ago by • 0 • written 3.8 years ago by • 0
1
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4
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2.6k
views
incorporating batch into DESeq2 design after batch correction with combatseq
DESeq2 sva
3.8 years ago Clay • 0
0
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1
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1.3k
views
Controlling for sex variance in Galaxy DESeq2
DESeq2 RNASeq Galaxy
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
2
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5
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2.5k
views
from kallisto to deseq2 analysis
biomaRt DESeq2 tximport
3.8 years ago Marianna ▴ 20
1
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7
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2.2k
views
Comparison DESeq results using different model
Batch BatchEffect DESeq2
updated 3.8 years ago by 68k • written 3.8 years ago by ▴ 10
0
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1
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2.4k
views
95% Confidence intervals for Fold Changes computed by DESeq2
DESeq2 RNASeq
updated 3.8 years ago by ★ 5.0k • written 3.8 years ago by • 0
0
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5
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1.5k
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DESeq2 - 50 vs 50 analysis
DESeq2
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
0
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3
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995
views
Differentially Paired RNA-Seq Analysis DESeq2
DESeq2
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
2
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3
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1.5k
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Import RSEM output without sample data
DESeq2 tximportData tximport
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
0
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2
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1.3k
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DEG analysis across multiple treatment condititions and different ages
DESeq2
3.8 years ago pqdugcsd • 0
2
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2
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2.1k
views
DESeq2: Size factor estimations for type = "poscounts" different between estimateSizeFactors() and estimateSizeFactorsForMatrix()
DESeq2
updated 3.8 years ago by 43k • written 3.8 years ago by ▴ 10
3
votes
1
reply
914
views
How to solve the "tilted tail" after DESeq2 normalization.
DESeq2
updated 3.8 years ago by ★ 5.0k • written 3.8 years ago by ▴ 20
0
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2
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1.2k
views
Extend comparisons between two groups to more groups in DESEQ2
edgeR DEGs DESEQ2 RNASeqData
3.8 years ago Raito92 ▴ 60
0
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6
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5.4k
views
Performing simple pairwise comparisons in DESEQ2
edgeR DEG RNASeq DESEQ2
updated 3.8 years ago by 43k • written 3.8 years ago by ▴ 60
4
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1
reply
1.6k
views
DEGs from lfcshrink() and results()
lfcshrink DESeq2
updated 3.8 years ago by ★ 5.0k • written 3.8 years ago by ▴ 10
0
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1
reply
1.1k
views
DESeq2 2x3 design contrast question
DESeq2 contrasts
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
0
votes
3
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1.2k
views
How to get DESeq2 results in large count matix files?
DESeq2 BiocParallel MulticoreParam
updated 3.8 years ago by 43k • written 3.8 years ago by ▴ 20
3
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5
replies
3.6k
views
Plot PC1 and PC4 in plotPCA function
DESeq2 plotPCA
updated 18 months ago by • 0 • written 3.8 years ago by • 0
0
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4
replies
1.9k
views
Multi-factor paired RNAseq differential analysis with DEseq2
DESeq2 RNASeq
updated 3.8 years ago by ★ 1.4k • written 3.8 years ago by • 0
1
vote
1
reply
1.6k
views
Swish with more than two conditions. Add support for contrasts?
tximeta DESeq2 swish fishpond
updated 3.8 years ago by 43k • written 3.8 years ago by ▴ 20
1
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3
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2.0k
views
ERROR: unable to find an inherited method for function ‘dispersions<-’ for signature ‘"DESeqDataSet",
DESeq2 dese
3.9 years ago • updated 3.8 years ago aedavids ▴ 20
0
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3
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3.4k
views
DESeq2 contrast multiple treated conditions versus multiple control conditions
RNASeq DESeq2
updated 3.8 years ago by ▴ 780 • written 3.9 years ago by • 0
1
vote
3
replies
2.1k
views
Correct use of Likelihood Ratio Test and LFC Shrinkage
RNASeq LRT DESeq2 lfcShrink
updated 2.8 years ago by • 0 • written 3.9 years ago by • 0
1
vote
4
replies
2.5k
views
Test if a gene is NOT differentially expressed in DESeq2?
DESeq2 deseq
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
0
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2
replies
1.4k
views
Removing paired samples for DESeq2 analysis
RNASeq DifferentialExpression DESeq2 tcga
3.9 years ago IamFrofro • 0
0
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4
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1.6k
views
Large DE LogFC range
DESeq2
updated 3.9 years ago by 43k • written 3.9 years ago by ▴ 20
0
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1
reply
1.1k
views
DESeq2 Responder vs Non-Responders nested design
paired-samples DESeq2 interactionterm nested-design
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
0
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5
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2.5k
views
Weird output of DESeq2 when using single sample from one group agains the other group (6 samples), really need some help
DifferentialExpression DESeq2
updated 3.9 years ago by 43k • written 3.9 years ago by ▴ 10
0
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1
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1.3k
views
DESeq2 differences in Wald and LRT in multi-factorial design
microbiome LRT DESeq2
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
0
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4
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1.8k
views
DE analysis model matrix for paired samples
NanoStringNCTools DESeq2
updated 3.9 years ago by 43k • written 3.9 years ago by ▴ 10
2
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3
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2.5k
views
Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data
NanoNormIter DifferentialExpression Housekeeping DESeq2 NanoString
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
1
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1
reply
1.3k
views
Unusal standard deviation after rlog transformation and the homoscedasticity of the data
rlog DESeq2 VST
updated 3.9 years ago by 43k • written 3.9 years ago by ▴ 10
0
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1
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1.3k
views
Deseq workflow for phyloseq object and complicated data structure?
phyloseq DESeq2
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
1
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2
replies
1.8k
views
Use of shrunken LFCs to address questions about the distribution of LFCs between gene categories.
deseq2 apeglm DESeq2
3.9 years ago i.sudbery ▴ 40
0
votes
2
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2.4k
views
PlotPCA in DESeq2 doesn't produce exactly the same result as prcomp
DESeq2 PCA
updated 3.9 years ago by ★ 1.4k • written 3.9 years ago by • 0
0
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2
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2.2k
views
rlog normalised count for comparing gene expression between samples
DESeq2
3.9 years ago Sam • 0
1
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2
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1.7k
views
rlog vs vst for outlier identification
rlog DESeq2 vst outliers
3.9 years ago Bex • 0
3
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5
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4.7k
views
DESeq2 median of ratios normalization for signature score calculation
MRN RNASeq Normalization DESeq2
updated 3.9 years ago by 43k • written 3.9 years ago by ▴ 10
3
votes
3
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1.7k
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 3.9 years ago by 43k • written 3.9 years ago by ▴ 120
0
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4
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1.1k
views
DESeq treatment over baseline versus placebo over baseline methodology
DESeq2
3.9 years ago walter.eckalbar • 0
1
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3
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2.4k
views
Transformations of the variance in RNA-seq count data DESeq2
RNASeq vst R rlog DESeq2
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
1
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2
replies
1.1k
views
DESeq2 expressed gene
DESeq2
3.9 years ago BioEpi • 0
0
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3
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1.3k
views
Same p-adjusted value for all samples
DESeq2 p-adjusted-value Logfoldchange
updated 3.9 years ago by 43k • written 3.9 years ago by ▴ 10
4
votes
5
replies
2.9k
views
Help with droplevels in Deseq2
droplevels DESeq2
updated 3.9 years ago by ★ 5.0k • written 3.9 years ago by ▴ 10
1
vote
8
replies
2.9k
views
DESeq2 analysis for targeted RNA-seq
DifferentialExpression DESeq2
3.9 years ago dadca596 • 0
3
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3
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10k
views
Adding sample label to PCA plot
plotpca DESeq2
3.9 years ago bjen731 ▴ 10
3
votes
5
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1.8k
views
P adjusted values in Deseq2
DESeq2 Statistics
written 4.9 years ago by • 0
1
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2
replies
4.9k
views
TPM to raw counts
salmon DESeq2
updated 2.0 years ago by • 0 • written 3.9 years ago by • 0
0
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1
reply
1.2k
views
Removal of sample data which belong to a different experiment
DESeq2
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
4,840 results • Page 24 of 97
Recent ...
Replies
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: 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
Votes
Upcoming Ensembl API and data access changes - new blog post available
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
Awards • All
Commentator to sina.nassiri ▴ 130
Popular Question to Hervé Pagès 16k
Popular Question to jared.andrews07 ▴ 30
Popular Question to James W. MacDonald 68k
Popular Question to shepherl 4.2k
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