Showing : DESeq2 • reset
16
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12
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8.4k
views
Diffbind: edgeR or DESeq2 ?
diffbind medip-seq edger deseq2
updated 6 months ago by • 0 • written 9.0 years ago by ▴ 60
0
votes
7
replies
1.1k
views
DESeq2 filtering vs edgeR filtering
DESeq2
12 months ago fr8712ca-s • 0
1
vote
5
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1.0k
views
RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 7 months ago by 52k • written 7 months ago by • 0
3
votes
11
replies
1.0k
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 5 months ago by • 0
6
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15
replies
1.7k
views
Deseq2 design formula and analysis with internal controls
DESeq2
updated 7 months ago by ★ 1.4k • written 7 months ago by • 0
4
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7
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1.6k
views
What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables DESeq2 BatchEffect bulkrna-seq sva-seq
updated 7 months ago by ▴ 10 • written 8 months ago by ▴ 70
1
vote
8
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1.3k
views
DEseq2 time-series design
deseq2
updated 5 months ago by ▴ 10 • written 6.0 years ago by • 0
0
votes
2
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1.1k
views
Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 6 months ago by ★ 1.4k • written 6 months ago by • 0
0
votes
3
replies
554
views
Ploting of normalized counts after batch removal
DESeq2
updated 9 months ago by 52k • written 9 months ago by ▴ 10
1
vote
8
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1.3k
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 8 months ago by 52k • written 9 months ago by • 0
2
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3
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1.1k
views
Analysis of large RNA-Seq Datasets
DESeq2
updated 5 months ago by 43k • written 5 months ago by • 0
34
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29
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16k
views
[DESeq2] time series strain-specific differences over time
deseq2 timecourse
updated 6 months ago by 43k • written 10.0 years ago by ▴ 130
3
votes
5
replies
1.5k
views
DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 7 months ago by ★ 1.4k • written 7 months ago by • 0
1
vote
3
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1.4k
views
Combining two bulk RNA seq datasets
RNASeqData DESeq2 Normalization
9 months ago Tanvi • 0
3
votes
7
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2.0k
views
Vertical line at A=0, nothing else, on MA plot
deseq2
updated 24 days ago by ▴ 10 • written 6.0 years ago by ▴ 20
0
votes
4
replies
1.2k
views
Higher Dimensional RNASeq Clustering Significance
DESeq2 RNASeq PrincipalComponent pcaExplorer
written 2.3 years ago by • 0
0
votes
6
replies
893
views
Counter-directional LFC shrinkage
DESeq2
updated 9 months ago by 43k • written 9 months ago by • 0
1
vote
4
replies
1.4k
views
Problem in running DESeq from expected count data of Transcriptome by Trinity followed by RSEM
Tissue Spati RSEM deno DEseq2
written 22 months ago by • 0
0
votes
5
replies
1.9k
views
DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 3.8 years ago by • 0
4
votes
2
replies
535
views
Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 3 months ago by ★ 4.7k • written 3 months ago by ▴ 10
0
votes
3
replies
668
views
Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 7 months ago by 52k • written 7 months ago by • 0
3
votes
6
replies
1.6k
views
[DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Application
DESeq2
updated 6 months ago by 43k • written 6 months ago by • 0
0
votes
4
replies
649
views
lfcShrink and alpha value
lfcShrink DESeq2
3 months ago cropero • 0
3
votes
6
replies
2.9k
views
Multiple factor DSEq2 result generates weird volcano plot
DESeq2
updated 9 months ago by ★ 4.7k • written 23 months ago by ▴ 20
1
vote
2
replies
2.4k
views
using tximport with STAR transcript-quantification output
tximport deseq2 STAR
updated 9 months ago by ▴ 40 • written 5.4 years ago by • 0
1
vote
5
replies
3.9k
views
DESeq2 swap ensembl gene id rownames with gene symbol column
deseq2 dataframe ensembl gene id gene symbol entrezid
updated 9 days ago by • 0 • written 5.3 years ago by ▴ 10
17
votes
9
replies
7.4k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 6 months ago by 68k • written 8.8 years ago by ▴ 10
2
votes
2
replies
475
views
Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 7 weeks ago by ★ 1.4k • written 8 weeks ago by • 0
0
votes
3
replies
695
views
comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 7 months ago by • 0
1
vote
6
replies
1.2k
views
Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 4 months ago by 43k • written 4 months ago by ▴ 10
0
votes
5
replies
689
views
p value is 0, padj is 0
DESeq2
3 months ago Wirayatida • 0
0
votes
4
replies
706
views
DEG with low counts
DESeq2
updated 11 months ago by 43k • written 11 months ago by • 0
9
votes
12
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8.9k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 11 months ago by • 0 • written 9.7 years ago by ▴ 30
5
votes
4
replies
664
views
How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 5 months ago by ★ 4.7k • written 5 months ago by • 0
0
votes
2
replies
409
views
DESeq2 v1.35.0
DESeq2
updated 10 months ago by 43k • written 10 months ago by • 0
3
votes
6
replies
29k
views
Deseq: What does "BaseMean" mean?
deseq2
written 6.5 years ago by • 0
2
votes
3
replies
697
views
DeSeq2 Model Problems with species, tissue, and tissue status nesting
DESeq2 R
written 8 months ago by • 0
2
votes
5
replies
434
views
Differential variability modelling with vst() expression
limma DESeq2
written 10 weeks ago by • 0
0
votes
5
replies
1.1k
views
Wondering how to look at the reads of a gene in samples to check if it was knocked out?
knockout DESeq2
written 21 months ago by • 0
2
votes
3
replies
807
views
Comparing one group against multiple groups in DESeq2
DESeq2
written 14 months ago by • 0
6
votes
3
replies
6.9k
views
DESeq2 with proteomics data
deseq2
updated 6 months ago by 43k • written 6.7 years ago by ▴ 10
0
votes
6
replies
862
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 10 months ago by ★ 1.4k • written 10 months ago by ▴ 130
4
votes
12
replies
1.3k
views
DGE with a Continuous Variable
DESeq2 model
updated 8 months ago by 43k • written 8 months ago by • 0
0
votes
2
replies
618
views
PCA analysis RNA-Seq QC looks strange?
DESeq2
updated 6 months ago by ★ 1.4k • written 6 months ago by • 0
2
votes
9
replies
1.0k
views
Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
10 weeks ago • updated 8 weeks ago Quang NN ▴ 10
2
votes
2
replies
776
views
Handling biological replicates in DESeq2
DESeq2
updated 4 months ago by ★ 4.7k • written 4 months ago by • 0
4
votes
5
replies
928
views
Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
updated 4 days ago by • 0 • written 18 days ago by • 0
0
votes
2
replies
469
views
Best way to describe DEseq2 design
DESeq2
updated 9 months ago by ★ 1.4k • written 9 months ago by • 0
6
votes
19
replies
4.5k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 10 months ago by • 0 • written 5.5 years ago by ▴ 10
4
votes
9
replies
1.7k
views
DESeq2 unable to handle large count values
DESeq2
updated 5 months ago by 43k • written 16 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: DiffBind custom normalization factor by Abbie • 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2? by James W. MacDonald 68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore by Michael Love 43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi by Michael Love 43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
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