Showing : DESeq2 • reset
52
votes
20
replies
48k
views
Batch correction in DESeq2
rnaseq batch effect deseq2 combat removebatcheffect()
updated 8.5 years ago by • 0 • written 9.0 years ago by ▴ 110
38
votes
21
replies
16k
views
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
deseq2
10.2 years ago • updated 2.2 years ago Michael Love 43k
34
votes
29
replies
15k
views
[DESeq2] time series strain-specific differences over time
deseq2 timecourse
updated 12 weeks ago by 43k • written 9.7 years ago by ▴ 130
32
votes
16
replies
19k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport deseq2 TPM RPKM rnaseq
updated 6.6 years ago by ▴ 20 • written 8.4 years ago by ▴ 200
30
votes
21
replies
55k
views
deseq2 filter the low counts
deseq2 lowcount
updated 10 months ago by • 0 • written 9.8 years ago by ▴ 40
28
votes
6
replies
43k
views
DESeq2: Is it possible to convert read counts to expression values via TPM and return these values?
deseq2 r
updated 2.7 years ago by ▴ 20 • written 7.9 years ago by ▴ 60
27
votes
7
replies
16k
views
Usability of ERCC spike-ins in standard RNAseq experiments
RNAseq deseq2 ercc
updated 8.1 years ago by ★ 3.8k • written 8.1 years ago by ▴ 30
27
votes
7
replies
12k
views
Effect of lfcThreshold on p-value in DESeq2
deseq2 rnaseq statistics
updated 14 months ago by ▴ 10 • written 7.2 years ago by ▴ 40
27
votes
22
replies
20k
views
DESeq2 for ChIP-seq differential peaks
deseq2 deseq chipseq
updated 7.4 years ago by ▴ 120 • written 9.2 years ago by ▴ 200
26
votes
17
replies
8.3k
views
DESeq2 1.20.0 lfcshrink function
deseq2 differential expression logfoldchange lfcshrink lfcthreshold
updated 3.5 years ago by 43k • written 6.5 years ago by ▴ 40
25
votes
7
replies
11k
views
Different logFC (log2foldchange) values for genes from limma-voom and other tools (edgeR and DESeq2)
limma deseq2 edger rnaseq
updated 7.2 years ago by 52k • written 7.2 years ago by ▴ 20
25
votes
11
replies
8.4k
views
Normalization methodology in DESeq/DESeq2 vs edgeR
deseq deseq2 edgeR normalization
updated 9.1 years ago by ★ 3.8k • written 9.1 years ago by ▴ 90
22
votes
12
replies
28k
views
New function lfcShrink() in DESeq2
deseq2
updated 5.3 years ago by • 0 • written 7.6 years ago by 43k
20
votes
15
replies
63k
views
DESeq2 output explanation
deseq deseq2
updated 3.1 years ago by 43k • written 10.1 years ago by ▴ 100
19
votes
7
replies
13k
views
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
deseq2 ensembl
updated 6.9 years ago by 67k • written 6.9 years ago by ▴ 170
18
votes
12
replies
4.1k
views
Low-count filtering with uneven sequencing depth between samples?
edgeR deseq2 rna-seq independent filtering
updated 9.5 years ago by 43k • written 9.5 years ago by ★ 7.9k
18
votes
4
replies
38k
views
Error in DESeqDataSet : some values in assay are not integers
deseq2 metagenomics
updated 4.3 years ago by ▴ 220 • written 4.3 years ago by ▴ 10
18
votes
4
replies
35k
views
FDR and padj in deseq and edger
deseq2 edger
updated 9.1 years ago by 52k • written 9.1 years ago by ▴ 80
17
votes
11
replies
37k
views
DESeq2 and shrinkage of log2 fold changes
deseq2
updated 5 months ago by 43k • written 8.9 years ago by ▴ 100
17
votes
7
replies
14k
views
DESeq2 lfcShrink() usage of coef vs. usage of contrast
deseq2 lfc coef contrast
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 10
17
votes
9
replies
7.0k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 11 weeks ago by 67k • written 8.5 years ago by ▴ 10
17
votes
13
replies
19k
views
deseq2 normalized data with heatmap
deseq2
updated 3.5 years ago by ▴ 10 • written 4.3 years ago by ▴ 20
16
votes
12
replies
3.0k
views
VST transformation (DESeq2) for metabolomics data
vst Metabolomics DESeq2
2.6 years ago Joan Miró ▴ 80
16
votes
19
replies
21k
views
DESeq2: add annotations (from data frame) to DESeqDataSet
deseq2 annotation granges
updated 2.8 years ago by ▴ 60 • written 10.1 years ago by ▴ 130
16
votes
40
replies
10k
views
Can NanoString data be analyzed using DESeq2?
NanoString Differential Expressed Genes Analysis DESeq2
updated 2.9 years ago by ▴ 10 • written 5.4 years ago by ▴ 50
16
votes
12
replies
7.7k
views
Diffbind: edgeR or DESeq2 ?
diffbind medip-seq edger deseq2
updated 3 months ago by • 0 • written 8.7 years ago by ▴ 60
15
votes
12
replies
72k
views
[DESEQ2] How to access the normalized data of a DESeqDataSet
deseq2
updated 9.7 years ago by ★ 13k • written 9.7 years ago by ▴ 130
15
votes
3
replies
2.0k
views
lfcShrink function for different comparison
DESeq2 RNASeq
updated 2.8 years ago by ▴ 30 • written 4.1 years ago by ▴ 90
15
votes
18
replies
4.1k
views
Is goana function for Gene Ontology enrichement analysis suitable for both edgeR and DESeq2 DEGs lists?
DESeq2 edgeR goana GO
updated 2.7 years ago by 52k • written 2.7 years ago by ▴ 60
15
votes
8
replies
11k
views
DESeq2 - Acquiring batch-corrected values for PCA and hierarchical clustering
deseq2 deseq
10.1 years ago salahm ▴ 70
15
votes
4
replies
3.2k
views
Using multiple tools for differential gene expression analysis as validation
edger limma deseq2 rnaseq
updated 8.4 years ago by ★ 7.9k • written 8.4 years ago by ▴ 130
15
votes
12
replies
2.8k
views
ZINB-WaVE + DESeq2 misses low-expressed, single-condition genes that look like they should be markers
deseq2 ZINB-WaVE single cell RNA-seq differential expression
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 60
14
votes
19
replies
9.4k
views
DESeq2 Model Design
DESeq2 linear model model
updated 3.6 years ago by 43k • written 10.0 years ago by ▴ 370
14
votes
5
replies
23k
views
Dealing with genes that have Padj=NA
deseq2
updated 16 months ago by • 0 • written 9.0 years ago by ▴ 60
14
votes
5
replies
45k
views
plotPCA - how to add labels to a PCA plot
plotPCA deseq2 labels
updated 7.9 years ago by ▴ 180 • written 7.9 years ago by ▴ 50
14
votes
9
replies
16k
views
How does DESeq2 handle zero counts in one condition?
deseq2 deseq rna-seq
9.9 years ago gavrielmatt ▴ 30
14
votes
22
replies
30k
views
DESEq2 Paired samples Before and after treatment
deseq2 paired samples
updated 9 months ago by 43k • written 8.5 years ago by ▴ 30
13
votes
6
replies
7.5k
views
DESeq2 multiple interaction terms 3-factor design
deseq2 deseq interactions multiple factor design
updated 8.9 years ago by 43k • written 8.9 years ago by ▴ 290
13
votes
16
replies
5.6k
views
Using edgeR or DESeq2 to analyze allele-specific expression?
edgeR deseq2 ase allele
9.2 years ago trianglescout ▴ 40
13
votes
10
replies
4.2k
views
Big differences in logfoldchange for some genes between edgeR and DESeq2
edger deseq2
updated 9.0 years ago by 52k • written 9.0 years ago by • 0
12
votes
1
reply
7.8k
views
identifying the samples on plotPCA
deseq2 plotpca PCa
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 80
12
votes
9
replies
11k
views
DESeq2 baseMean values for each sample
deseq2
10.0 years ago aburkha69 ▴ 30
12
votes
11
replies
4.7k
views
Memory usage for bplapply -- is the entire environment copied over to each worker thread?
bplapply biocparallel deseq2
updated 9.4 years ago by ★ 6.8k • written 9.4 years ago by ▴ 40
12
votes
6
replies
22k
views
DESEq2 comparison with mulitple cell types under 2 conditions
deseq2 multiple factor design
updated 9.6 years ago by 43k • written 9.6 years ago by ▴ 50
12
votes
6
replies
3.7k
views
Allele Specific Expression in DESeq2 or EdgeR
rnaseq deseq2 edger
9.0 years ago martiningi ▴ 40
12
votes
8
replies
2.3k
views
DESeq fitted values using coefficients vs mu
deseq2
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 830
12
votes
14
replies
29k
views
DESeq2 normalization vs VST vs rlog
deseq2
updated 2.0 years ago by • 0 • written 5.3 years ago by ▴ 40
12
votes
4
replies
4.4k
views
WGCNA following salmon/DESeq2
deseq2 wgcna salmon
updated 6.0 years ago by ★ 3.0k • written 6.0 years ago by ▴ 30
12
votes
18
replies
6.0k
views
What is the correct use of removeBatchEffect's design parameter
deseq2 limma
updated 3.7 years ago by 52k • written 4.2 years ago by ▴ 10
11
votes
3
replies
3.6k
views
Testing three-way interactions in DESeq2
deseq2 rna-seq rnaseq interactions
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 60
50 results • Page 1 of 1
Recent ...
Replies
Answer: RSubread output significantly different from bash Subread output by Gordon Smyth 52k
The difference (as ATpoint has correctly pointed out) is that Rsubread::featureCounts counts multi-mapping reads by default whereas the com…
Answer: Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square by Michael Love 43k
I would check the rank of your model matrix, and perhaps meet with a local statistician who can help you create an appropriate design matri…
Comment: sva: get a sv for RIN scores by gabriel.hoffman ▴ 170
Agreed. I'll add that with small sample size, a covariate can explain some fraction of expression variation even under the null.
Comment: RSubread output significantly different from bash Subread output by Aimee • 0
Thank you! I will try rerunning with that parameter and see if it fixes the discrepancy! I'll report back. Update: This completely resolve…
Answer: RSubread output significantly different from bash Subread output by ATpoint ★ 4.6k
The R version counts multimappers (countMultiMappingReads is TRUE by default) while the command line version does not. It's beyond me why t…
Votes
Answer: RSubread output significantly different from bash Subread output
Answer: RSubread output significantly different from bash Subread output
Answer: How to annotate a limma Elist raw class object with an annotation file
Comment: How to annotate a limma Elist raw class object with an annotation file
QSEA- Extraction of Normalized methylation across the samples
Awards • All
Teacher to Michael Love 43k
Popular Question to Dario Strbenac ★ 1.5k
Scholar to ATpoint ★ 4.6k
Popular Question to Gordon Smyth 52k
Popular Question to bhandary.8590 ▴ 20
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