Showing : DESeq2 • reset
52
votes
20
replies
40k
views
Batch correction in DESeq2
rnaseq batch effect deseq2 combat removebatcheffect()
updated 7.3 years ago by • 0 • written 7.8 years ago by ▴ 110
33
votes
21
replies
13k
views
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
deseq2
9.0 years ago • updated 12 months ago Michael Love 40k
32
votes
16
replies
16k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport deseq2 TPM RPKM rnaseq
updated 5.4 years ago by ▴ 20 • written 7.2 years ago by ▴ 190
27
votes
18
replies
42k
views
deseq2 filter the low counts
deseq2 lowcount
updated 5 days ago by • 0 • written 8.6 years ago by ▴ 30
26
votes
22
replies
17k
views
DESeq2 for ChIP-seq differential peaks
deseq2 deseq chipseq
updated 6.3 years ago by ▴ 120 • written 8.1 years ago by ▴ 190
25
votes
7
replies
9.0k
views
Effect of lfcThreshold on p-value in DESeq2
deseq2 rnaseq statistics
updated 12 hours ago by ▴ 10 • written 6.0 years ago by ▴ 30
25
votes
11
replies
7.2k
views
Normalization methodology in DESeq/DESeq2 vs edgeR
deseq deseq2 edgeR normalization
updated 7.9 years ago by ★ 3.7k • written 7.9 years ago by ▴ 80
24
votes
6
replies
34k
views
DESeq2: Is it possible to convert read counts to expression values via TPM and return these values?
deseq2 r
updated 18 months ago by ▴ 20 • written 6.7 years ago by ▴ 50
24
votes
7
replies
13k
views
Usability of ERCC spike-ins in standard RNAseq experiments
RNAseq deseq2 ercc
updated 7.0 years ago by ★ 3.7k • written 7.0 years ago by ▴ 30
21
votes
7
replies
8.0k
views
Different logFC (log2foldchange) values for genes from limma-voom and other tools (edgeR and DESeq2)
limma deseq2 edger rnaseq
updated 6.0 years ago by 48k • written 6.0 years ago by • 0
21
votes
17
replies
6.2k
views
DESeq2 1.20.0 lfcshrink function
deseq2 differential expression logfoldchange lfcshrink lfcthreshold
updated 2.4 years ago by 40k • written 5.3 years ago by ▴ 20
21
votes
12
replies
23k
views
New function lfcShrink() in DESeq2
deseq2
updated 4.1 years ago by • 0 • written 6.4 years ago by 40k
18
votes
24
replies
13k
views
[DESeq2] time series strain-specific differences over time
deseq2 timecourse
updated 2.6 years ago by • 0 • written 8.6 years ago by ▴ 120
18
votes
12
replies
3.3k
views
Low-count filtering with uneven sequencing depth between samples?
edgeR deseq2 rna-seq independent filtering
updated 8.3 years ago by 40k • written 8.3 years ago by 7.8k
18
votes
4
replies
30k
views
FDR and padj in deseq and edger
deseq2 edger
updated 7.9 years ago by 48k • written 7.9 years ago by ▴ 80
17
votes
9
replies
29k
views
DESeq2 and shrinkage of log2 fold changes
deseq2
updated 2.7 years ago by 40k • written 7.7 years ago by ▴ 100
17
votes
15
replies
53k
views
DESeq2 output explanation
deseq deseq2
updated 23 months ago by 40k • written 8.9 years ago by ▴ 100
16
votes
7
replies
12k
views
DESeq2 lfcShrink() usage of coef vs. usage of contrast
deseq2 lfc coef contrast
updated 6.2 years ago by 40k • written 6.2 years ago by ▴ 10
16
votes
7
replies
10k
views
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
deseq2 ensembl
updated 5.7 years ago by 63k • written 5.7 years ago by ▴ 150
16
votes
40
replies
6.8k
views
Can NanoString data be analyzed using DESeq2?
NanoString Differential Expressed Genes Analysis DESeq2
updated 21 months ago by • 0 • written 4.2 years ago by ▴ 50
16
votes
9
replies
5.7k
views
Diffbind: edgeR or DESeq2 ?
diffbind medip-seq edger deseq2
updated 5.9 years ago by ★ 5.0k • written 7.6 years ago by ▴ 60
15
votes
12
replies
59k
views
[DESEQ2] How to access the normalized data of a DESeqDataSet
deseq2
updated 8.5 years ago by 13k • written 8.5 years ago by ▴ 120
15
votes
12
replies
2.2k
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 5.1 years ago by 40k • written 5.1 years ago by ▴ 60
15
votes
8
replies
10k
views
DESeq2 - Acquiring batch-corrected values for PCA and hierarchical clustering
deseq2 deseq
8.9 years ago salahm ▴ 70
15
votes
4
replies
2.4k
views
Using multiple tools for differential gene expression analysis as validation
edger limma deseq2 rnaseq
updated 7.3 years ago by 7.8k • written 7.3 years ago by ▴ 130
15
votes
7
replies
5.0k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 7.3 years ago by 7.8k • written 7.3 years ago by ▴ 10
15
votes
13
replies
12k
views
deseq2 normalized data with heatmap
deseq2
updated 2.3 years ago by ▴ 10 • written 3.1 years ago by ▴ 20
15
votes
18
replies
2.4k
views
Is goana function for Gene Ontology enrichement analysis suitable for both edgeR and DESeq2 DEGs lists?
DESeq2 edgeR goana GO
updated 18 months ago by 48k • written 18 months ago by ▴ 60
14
votes
19
replies
8.4k
views
DESeq2 Model Design
DESeq2 linear model model
updated 2.4 years ago by 40k • written 8.9 years ago by ▴ 370
14
votes
4
replies
26k
views
Error in DESeqDataSet : some values in assay are not integers
deseq2 metagenomics
updated 3.1 years ago by ▴ 180 • written 3.1 years ago by ▴ 10
14
votes
19
replies
18k
views
DESeq2: add annotations (from data frame) to DESeqDataSet
deseq2 annotation granges
updated 20 months ago by ▴ 50 • written 8.9 years ago by ▴ 120
14
votes
5
replies
36k
views
plotPCA - how to add labels to a PCA plot
plotPCA deseq2 labels
updated 6.7 years ago by ▴ 150 • written 6.7 years ago by ▴ 50
14
votes
9
replies
13k
views
How does DESeq2 handle zero counts in one condition?
deseq2 deseq rna-seq
8.7 years ago gavrielmatt ▴ 30
13
votes
16
replies
4.4k
views
Using edgeR or DESeq2 to analyze allele-specific expression?
edgeR deseq2 ase allele
8.0 years ago trianglescout ▴ 40
13
votes
5
replies
20k
views
Dealing with genes that have Padj=NA
deseq2
updated 8 weeks ago by • 0 • written 7.8 years ago by ▴ 60
13
votes
6
replies
6.6k
views
DESeq2 multiple interaction terms 3-factor design
deseq2 deseq interactions multiple factor design
updated 7.7 years ago by 40k • written 7.7 years ago by ▴ 290
13
votes
10
replies
3.5k
views
Big differences in logfoldchange for some genes between edgeR and DESeq2
edger deseq2
updated 7.8 years ago by 48k • written 7.8 years ago by • 0
12
votes
6
replies
20k
views
DESEq2 comparison with mulitple cell types under 2 conditions
deseq2 multiple factor design
updated 8.4 years ago by 40k • written 8.4 years ago by ▴ 50
12
votes
6
replies
3.0k
views
Allele Specific Expression in DESeq2 or EdgeR
rnaseq deseq2 edger
7.9 years ago martiningi ▴ 40
12
votes
8
replies
1.6k
views
DESeq fitted values using coefficients vs mu
deseq2
updated 6.7 years ago by 40k • written 6.7 years ago by ▴ 830
12
votes
11
replies
3.7k
views
Memory usage for bplapply -- is the entire environment copied over to each worker thread?
bplapply biocparallel deseq2
updated 8.2 years ago by ★ 6.8k • written 8.2 years ago by ▴ 40
12
votes
1
reply
6.5k
views
identifying the samples on plotPCA
deseq2 plotpca PCa
updated 6.0 years ago by 40k • written 6.0 years ago by ▴ 80
11
votes
8
replies
7.8k
views
Pre-processing of RNA-Seq data for WGCNA and DGE
WGCNA RNA-Seq DESeq2 voom removebatcheffect()
updated 7.0 years ago by ★ 2.8k • written 7.0 years ago by ▴ 70
11
votes
18
replies
3.6k
views
What is the correct use of removeBatchEffect's design parameter
deseq2 limma
updated 2.5 years ago by 48k • written 3.1 years ago by ▴ 10
11
votes
10
replies
3.6k
views
Is it appropriate to use DESeq2 to analyse MinION data that's been mapped to a transcriptome?
deseq2 nanopore
4.4 years ago David Eccles (gringer) ▴ 30
11
votes
14
replies
10.0k
views
Is there a conceptual difference between vst/rlog transforms and lfcShrink?
deseq2
updated 5.7 years ago by 40k • written 5.7 years ago by ▴ 40
11
votes
3
replies
1.2k
views
lfcShrink function for different comparison
DESeq2 RNASeq
updated 20 months ago by ▴ 30 • written 2.9 years ago by ▴ 60
11
votes
7
replies
15k
views
DESeq2: multiple conditions design -- How to select subset comparisons from the DESeq object for PCA, ...
deseq2
updated 23 months ago by 40k • written 7.6 years ago by ▴ 20
11
votes
4
replies
32k
views
DESeq2 baseMean counts
deseq2
updated 7.9 years ago by 40k • written 7.9 years ago by • 0
11
votes
1
reply
14k
views
Deseq2: RNA-seq and Negative binomial distribution
rnaseq deseq2
updated 7.9 years ago by 40k • written 7.9 years ago by ▴ 20
50 results • Page 1 of 1
Recent ...
Replies
Comment: Exporting DESeq2 filtered results by James W. MacDonald 63k
I am interested to know what part of my response you found rude. I asked nicely that you don't add to ancient posts, said your post isn't r…
Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
> I can imagine writing a sparse high-dimensional array in HDF5, but I'm still not sure how to implement the part where it is read and imme…
Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
Not in BioC 3.18. At some point (e.g. in 6 months) they will be deprecated, then 6 months later (i.e. in 1 year) they will be defunct, then…
Comment: Biostrings error at retrieving protein sequences by Hervé Pagès 16k
Yes, but you need to put the clean names back on the AAStringSet object: ``` names(protein_sequences) <- gsub(" .*", "", names(protein_sequ…
Comment: Exporting DESeq2 filtered results by camillab. ▴ 10
thanks! I didn't`t notice that. I will cancel it now!
Votes
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
A: BiomaRt Arabidopsis genome unavailable
Answer: enrichKEGG
A: Effect of lfcThreshold on p-value in DESeq2
Comment: Mixed up sample info with plotPCA
Awards • All
Popular Question to Yahan • 0
Popular Question to Gordon Smyth 48k
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Popular Question to James W. MacDonald 63k
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