Showing : DEseq • reset
40
votes
44
replies
9.2k
views
Are published RNA seq data analyses often wrong in calculating p-values and FDR?
FDR p-value DESeq RNA-Seq
updated 5.8 years ago by ▴ 60 • written 6.4 years ago by ▴ 10
26
votes
22
replies
17k
views
DESeq2 for ChIP-seq differential peaks
deseq2 deseq chipseq
updated 6.2 years ago by ▴ 120 • written 8.0 years ago by ▴ 190
25
votes
11
replies
7.2k
views
Normalization methodology in DESeq/DESeq2 vs edgeR
deseq deseq2 edgeR normalization
updated 7.8 years ago by ★ 3.7k • written 7.9 years ago by ▴ 80
17
votes
15
replies
53k
views
DESeq2 output explanation
deseq deseq2
updated 22 months ago by 40k • written 8.9 years ago by ▴ 100
16
votes
5
replies
6.9k
views
DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
limma voom deseq normalization ercc
updated 7.8 years ago by 48k • written 7.8 years ago by ▴ 110
15
votes
8
replies
10k
views
DESeq2 - Acquiring batch-corrected values for PCA and hierarchical clustering
deseq2 deseq
8.9 years ago salahm ▴ 70
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
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
10
votes
14
replies
3.6k
views
Why limma, edgeR, and DESeq did not implement fold change moderation first?
limma edger deseq deseq2
updated 6.0 years ago by 48k • written 6.0 years ago by ▴ 80
10
votes
14
replies
11k
views
how DESeq calculates p-value ?
deseq differential gene expression statistics p-value
updated 2.5 years ago by ▴ 20 • written 7.6 years ago by ▴ 30
9
votes
6
replies
8.9k
views
Error bars DESeq or DESeq2 fold change
rnaseq deseq2 deseq standard error confidence interval
updated 22 months ago by 40k • written 7.5 years ago by ▴ 10
9
votes
17
replies
1.4k
views
DESeq2 design subcategories
deseq2 deseq differential binding analysis
updated 5.8 years ago by 40k • written 5.8 years ago by ▴ 60
8
votes
4
replies
1.8k
views
DESeq2: interaction term as in limma
deseq2 deseq limma interaction term
updated 6.4 years ago by ★ 3.7k • written 6.4 years ago by ▴ 80
8
votes
3
replies
4.0k
views
DESeq2 with interaction using SVA
deseq2 sva interaction term grouping variable deseq
5.7 years ago kevin.kingsland ▴ 70
8
votes
2
replies
2.5k
views
Statistical analysis of Spectral count data : edgeR, limma or others ?
spectral counts proteomics limma edger deseq
updated 8.2 years ago by 48k • written 8.2 years ago by ▴ 60
7
votes
12
replies
8.5k
views
Confused in the usage of formula in DESeq or DESeq2
deseq2 deseq
updated 6.3 years ago by ▴ 60 • written 8.9 years ago by ▴ 20
7
votes
18
replies
7.5k
views
Differential expression analysis: Continuous variables
DESeq EdgeR limma
8.0 years ago Radek ▴ 90
6
votes
12
replies
15k
views
Problem making DESeq dataset; Error all variables in design formula must be columns in colData
deseq2 deseq counts rnaseq differential gene expression
updated 7.4 years ago by 40k • written 7.4 years ago by ▴ 10
6
votes
7
replies
3.5k
views
RUVseq PCA on raw data, whereas DESeq suggests stabilization
ruvseq deseq
7.8 years ago tonja.r ▴ 80
5
votes
11
replies
25k
views
With DESeq2 "Not full rank" Error with design ~ line + time + condition
deseq deseq2
updated 7 weeks ago by • 0 • written 8.7 years ago by ▴ 30
5
votes
2
replies
1.2k
views
Is the VST implemented in DESeq useful on time-series cell differentiation datasets?
deseq deseq2 vst
updated 6.4 years ago by 13k • written 6.4 years ago by • 0
5
votes
3
replies
6.7k
views
What problem does the MA plot diagnose? And how do you solve it?
deseq2 deseq rnaseq
updated 6.6 years ago by 7.8k • written 6.6 years ago by ▴ 40
5
votes
13
replies
5.1k
views
P values from Deseq Analysis
deseq
6.4 years ago Shrikant Pawar • 0
4
votes
1
reply
13k
views
The latest version of R is 3.5.1 and it is not compatible with many Bioconductor packages.
R deseq tcgabiolinks
5.1 years ago ansari.sarabio • 0
4
votes
7
replies
3.0k
views
Deseq2 design for one condition over 8 different time point
deseq2 rna-seq design matrix deseq
updated 5.0 years ago by 40k • written 5.0 years ago by • 0
4
votes
6
replies
1.2k
views
DESeq2 design and stats question
deseq2 differential binding analysis deseq atac-seq
updated 5.7 years ago by 40k • written 5.7 years ago by ▴ 60
4
votes
3
replies
2.4k
views
Why does Deseq, Deseq2, and EdgeR give vastly different results.
edger deseq deseq2
6.3 years ago michael.steffen ▴ 20
4
votes
2
replies
7.4k
views
Analyzing RNA-Seq data without replicates using DESeq
deseq DESeq2
updated 9.0 years ago by 40k • written 9.0 years ago by ▴ 90
4
votes
3
replies
3.2k
views
Add new columns to DESeqResults from text file by matching rownames.
deseq2 deseq merge data frames cbind s4vectors
updated 6.0 years ago by 40k • written 6.0 years ago by • 0
4
votes
14
replies
15k
views
standard error value (lfcSE) returned by DeSeq2
deseq2 deseq lfc lfcse standard error
updated 6.5 years ago by • 0 • written 6.5 years ago by • 0
4
votes
6
replies
1.3k
views
Interpretation of DESeq2 results with 3 factorial design with interaction terms.
r DESeq DESeq2
24 months ago s-rhussien • 0
4
votes
4
replies
3.6k
views
TMM Normalization: DESeqDataSet: some values in assay are negative
deseq2 deseq normalization
updated 4.1 years ago by ▴ 40 • written 4.2 years ago by • 0
4
votes
7
replies
1.1k
views
Filtering DESeq2 result export along multiple lines
deseq2 differential binding analysis deseq
updated 5.9 years ago by 40k • written 5.9 years ago by ▴ 60
3
votes
4
replies
3.0k
views
Variance filtering prior to RNA-seq differential expression
sequencing deseq limma
updated 8.2 years ago by 48k • written 8.2 years ago by ▴ 410
3
votes
7
replies
914
views
The discrepancy between the mean of extracted fitted value and calculated mean and SE based on LFC.
deseq2 deseq
5.1 years ago blastzone.heimerdinger ▴ 10
3
votes
5
replies
6.7k
views
DESeq2 resultsNames output
deseq deseq2
updated 8.6 years ago by 40k • written 8.6 years ago by ▴ 40
3
votes
7
replies
1.9k
views
novice: building gene co-expression network using RNA-Seq data
rna-seq WGCNA deseq method coexpression
updated 5.4 years ago by ★ 2.8k • written 5.4 years ago by ▴ 10
3
votes
3
replies
1.8k
views
read counts of paired end reads for DESeq2 analysis
deseq featurecounts paired
updated 7.4 years ago by 13k • written 7.4 years ago by • 0
3
votes
14
replies
17k
views
Normalization in DESeq2
deseq2 deseq
updated 8.8 years ago by 40k • written 8.8 years ago by ▴ 90
3
votes
4
replies
2.8k
views
DESeq is better than DESeq2?
deseq2 deseq
7.5 years ago ribioinfo ▴ 100
3
votes
12
replies
1.2k
views
Why did I get NA p-values in DESeq with continuous variable?
deseq2 p-value continuous deseq
4.6 years ago ariel ▴ 10
3
votes
11
replies
3.0k
views
DESeq function taking too long
deseq2 deseq factor rnaseq
updated 6.2 years ago by ★ 2.8k • written 6.2 years ago by ▴ 30
3
votes
1
reply
5.7k
views
Deseq for pairwise comparison among many pairs
DESeq DESeq
updated 9.3 years ago by 40k • written 9.3 years ago by ▴ 20
3
votes
8
replies
4.0k
views
DESeq / DESeq2 for translation efficiency in polysome profiling or ribsome profiling experiments
Sequencing DESeq Sequencing DESeq
updated 7.1 years ago by • 0 • written 9.8 years ago by ★ 12k
3
votes
1
reply
1.1k
views
RNASeq testing for differential expression in one condition, equality in another (using DESeq)
deseq2 deseq rnaseq
6.6 years ago ysdel ▴ 40
3
votes
2
replies
11k
views
how to get normalized counts from edgeR
DESeq DESeq
updated 11.2 years ago by ▴ 880 • written 11.2 years ago by ★ 2.0k
3
votes
5
replies
2.1k
views
DESeq on transcripts v/s genes
DESeq DESeq
updated 11.6 years ago by 13k • written 11.6 years ago by ▴ 410
3
votes
5
replies
2.5k
views
Using DESeq2: experimental design and extracting results
DESeq DESeq2 DESeq DESeq2
updated 9.3 years ago by 40k • written 9.3 years ago by ▴ 60
3
votes
2
replies
2.7k
views
Nanostring ncounterdata - DESeq
RNASeq Normalization Preprocessing DESeq RNASeq Normalization Preprocessing DESeq
updated 12.2 years ago by ★ 3.7k • written 12.2 years ago by ▴ 20
3
votes
5
replies
4.5k
views
Labeling points with hgnc symbols on the MA plot in DESeq2
deseq MA
updated 7.2 years ago by ▴ 150 • written 7.2 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: DMRcate design by Jitendra ▴ 10
Thanks James, do I also need to mention 'contrasts=FALSE' in cpg.annotate.And also what to mentions in analysis.type="differential",/ "ANO…
Comment: Speeding up of DelayedArray::write_block() by Koki ▴ 10
I don't know the details but do you mean using `HDF5RealizationSink` or `TENxRealizationSink` will make it possible to writing sparse multi…
Comment: DelayedArray::read_sparse_block by Koki ▴ 10
Ok, I understood. How about "writing" to HDF5? Are you going to implement `write_block_as_sparse` in `SparseArray` package?
Comment: DelayedArray::read_sparse_block by Hervé Pagès 16k
> So do you means the specification change from DelayedArray's read_sparse_block to SparseArray's read_block_as_sparse will accelerate the …
Comment: DelayedArray::read_sparse_block by Koki ▴ 10
Thanks for your reply. So do you means the specification change from `DelayedArray`'s `read_sparse_block` to `SparseArray`'s `read_block_a…
Votes
Steps needed to change design (relevel factors) in DESeq2
Steps needed to change design (relevel factors) in DESeq2
Answer: DMRcate design
Answer: DMRcate design
Comment: DMRcate design
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