Showing : DESeq2 • reset
17
votes
11
replies
39k
views
DESeq2 and shrinkage of log2 fold changes
deseq2
updated 9 months ago by 43k • written 9.2 years ago by ▴ 100
3
votes
6
replies
29k
views
Deseq: What does "BaseMean" mean?
deseq2
written 6.5 years ago by • 0
5
votes
3
replies
27k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 6.2 years ago by ▴ 30
10
votes
20
replies
24k
views
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
deseq2 batch effect batch
updated 5 months ago by 68k • written 5.8 years ago by ▴ 30
38
votes
23
replies
17k
views
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
deseq2
10.5 years ago • updated 2 days ago Michael Love 43k
34
votes
29
replies
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
0
votes
9
replies
16k
views
How to generate a volcano plot when p-values from DESeq2 are zero?
deseq2 pvalue visualization enhancedvolcano rnaseq
written 6.1 years ago by • 0
9
votes
12
replies
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
16
votes
12
replies
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
8
votes
5
replies
7.5k
views
Understanding interaction term in DESeq2
deseq2 design formula log fold change
updated 7 months ago by 43k • written 4.6 years ago by ▴ 40
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
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
1
vote
7
replies
6.6k
views
DESeq2 with unbalanced experimental design
deseq2
updated 4 months ago by • 0 • written 10.0 years ago by • 0
5
votes
29
replies
5.2k
views
DESeq2 model - How to test case/control time course model when taking account within sample variability?
deseq2 multiple time points time course casecontrol model design
updated 2 days ago by 43k • written 7.7 years ago by ▴ 10
2
votes
3
replies
4.8k
views
Deseq2 use fpkm
deseq2
updated 8 months ago by 43k • written 8.4 years ago by ▴ 40
1
vote
3
replies
4.5k
views
Log2 fold change value in DESeq2
deseq2 rnaseq
written 7.4 years 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
0
votes
8
replies
4.4k
views
DESeq2: handling NA values in colData
deseq2 coldata NA
updated 7 months ago by 43k • written 6.6 years ago by ▴ 170
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
1
vote
8
replies
3.7k
views
Significantly regulated genes produced by only a few affected samples
deseq2
written 7.0 years ago by ▴ 60
3
votes
5
replies
3.3k
views
Plot PC1 and PC4 in plotPCA function
DESeq2 plotPCA
updated 9 months ago by • 0 • written 3.1 years ago by • 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
6
votes
5
replies
2.7k
views
What is the importance of `--countReadPairs` in featureCounts on paired end data?
featureCounts DESeq2
updated 11 weeks ago by ▴ 20 • written 7 months ago by • 0
1
vote
2
replies
2.6k
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
11 months ago Patadù ▴ 20
1
vote
2
replies
2.5k
views
Why does DESeq2 give negative log2 fold change in treatment vs control for some genes when normalized counts are higher in treatment.
DESeq2
9 months ago sropri • 0
0
votes
2
replies
2.5k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2 SpikeIn Normalization
updated 10 months ago by • 0 • written 2.2 years ago by ▴ 10
1
vote
3
replies
2.4k
views
ColData and ERROR: rows did not converge in beta, labelled in mcols(object)$betaConv. Use larger maxit argument with nbinomWaldTest
DESeq2
updated 4 months ago by 43k • written 2.7 years ago by • 0
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
3
replies
2.3k
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 10 months ago by ★ 4.7k • written 10 months ago by • 0
1
vote
5
replies
2.3k
views
how to plot multiple RLEs on same plot?
plotRLE Nanostring RUVSeq DESEQ2
updated 7 months ago by ▴ 70 • written 3.8 years ago by ▴ 50
3
votes
4
replies
2.2k
views
How to formulate 2 factor nested design in DESeq2
nested_design RNASeqData DESeq2
updated 4 weeks ago by • 0 • written 2.8 years ago by ▴ 20
1
vote
9
replies
2.2k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 9 months ago by 68k • written 9 months ago by ▴ 10
2
votes
7
replies
2.2k
views
DeSeq2 - Can't fetch any results: Error in .wrap_in_length_one_list_like_object(value, name, x)
deseq2 software error
updated 4 months ago by • 0 • written 5.3 years ago by ▴ 30
5
votes
3
replies
2.1k
views
DeSeq2 Comparing One group vs Two groups
DESeq2
written 3.4 years ago by ▴ 10
1
vote
8
replies
2.1k
views
DESeq2 test for synergistic vs additive effects
synergistic additive DESeq2
updated 11 months ago by ★ 13k • written 21 months ago by ▴ 10
0
votes
7
replies
2.1k
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 11 months ago by ★ 1.4k • written 11 months ago by • 0
2
votes
3
replies
2.0k
views
Plot PCA with ellipses using ggplot
DESeq2 ggplot PCA
written 7 months ago by • 0
3
votes
7
replies
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
6
replies
2.0k
views
DESeq2 It is correct to use interaction term for patient variability?
deseq2 design interaction term R
written 7.1 years ago by • 0
2
votes
3
replies
1.9k
views
How to convert transcript counts to gene counts in R?
DESeq2 tximport
written 2.4 years ago by ▴ 50
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
5
replies
1.9k
views
Adding cell population estimates as a covariate in DESeq2 differential gene expression analysis
DESeq2 Dese DifferentialRegulation differe
updated 9 months ago by • 0 • written 23 months ago by ▴ 10
2
votes
5
replies
1.9k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 11 months ago by • 0 • written 21 months ago by • 0
1
vote
6
replies
1.9k
views
how to analysis htseq-count
deseq2
written 7.2 years ago by ▴ 30
1
vote
5
replies
1.8k
views
p-value the same for different contrasts DESeq2
deseq2 design and contrast matrix
updated 5 weeks ago by • 0 • written 6.9 years ago by ▴ 10
6
votes
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
0
votes
9
replies
1.7k
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 9 months ago by ▴ 70 • written 10 months ago by • 0
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
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
1.6k
views
Volcano plot of scRNA-seq data not "centered"
DESeq2
updated 10 months ago by ★ 4.7k • written 10 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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