Showing : DEseq • reset
41
votes
44
replies
12k
views
Are published RNA seq data analyses often wrong in calculating p-values and FDR?
FDR p-value DESeq RNA-Seq
updated 7.0 years ago by ▴ 60 • written 7.6 years ago by ▴ 10
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
25
votes
11
replies
8.4k
views
Normalization methodology in DESeq/DESeq2 vs edgeR
deseq deseq2 edgeR normalization
updated 9.0 years ago by ★ 3.8k • written 9.0 years ago by ▴ 90
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
16
votes
5
replies
7.9k
views
DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
limma voom deseq normalization ercc
updated 9.0 years ago by 52k • written 9.0 years ago by ▴ 120
15
votes
8
replies
11k
views
DESeq2 - Acquiring batch-corrected values for PCA and hierarchical clustering
deseq2 deseq
10.1 years ago • updated 10.0 years ago salahm ▴ 70
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
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
10
votes
14
replies
5.0k
views
Why limma, edgeR, and DESeq did not implement fold change moderation first?
limma edger deseq deseq2
updated 7.2 years ago by 52k • written 7.2 years ago by ▴ 90
10
votes
14
replies
14k
views
how DESeq calculates p-value ?
deseq differential gene expression statistics p-value
updated 3.7 years ago by ▴ 20 • written 8.8 years ago by ▴ 30
9
votes
6
replies
11k
views
Error bars DESeq or DESeq2 fold change
rnaseq deseq2 deseq standard error confidence interval
updated 3.1 years ago by 43k • written 8.6 years ago by ▴ 10
9
votes
17
replies
2.0k
views
DESeq2 design subcategories
deseq2 deseq differential binding analysis
updated 7.0 years ago by 43k • written 7.0 years ago by ▴ 60
8
votes
4
replies
2.3k
views
DESeq2: interaction term as in limma
deseq2 deseq limma interaction term
updated 7.6 years ago by ★ 3.8k • written 7.6 years ago by ▴ 80
8
votes
2
replies
3.2k
views
Statistical analysis of Spectral count data : edgeR, limma or others ?
spectral counts proteomics limma edger deseq
updated 9.4 years ago by 52k • written 9.4 years ago by ▴ 70
8
votes
3
replies
5.3k
views
DESeq2 with interaction using SVA
deseq2 sva interaction term grouping variable deseq
6.8 years ago kevin.kingsland ▴ 70
7
votes
12
replies
9.3k
views
Confused in the usage of formula in DESeq or DESeq2
deseq2 deseq
updated 7.5 years ago by ▴ 60 • written 10.1 years ago by ▴ 20
7
votes
18
replies
9.1k
views
Differential expression analysis: Continuous variables
DESeq EdgeR limma
9.2 years ago Radek ▴ 90
6
votes
12
replies
18k
views
Problem making DESeq dataset; Error all variables in design formula must be columns in colData
deseq2 deseq counts rnaseq differential gene expression
updated 8.6 years ago by 43k • written 8.6 years ago by ▴ 10
6
votes
11
replies
27k
views
With DESeq2 "Not full rank" Error with design ~ line + time + condition
deseq deseq2
updated 16 months ago by • 0 • written 9.9 years ago by ▴ 40
6
votes
7
replies
4.4k
views
RUVseq PCA on raw data, whereas DESeq suggests stabilization
ruvseq deseq
9.0 years ago tonja.r ▴ 80
6
votes
3
replies
4.2k
views
Add new columns to DESeqResults from text file by matching rownames.
deseq2 deseq merge data frames cbind s4vectors
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 20
5
votes
7
replies
4.0k
views
Deseq2 design for one condition over 8 different time point
deseq2 rna-seq design matrix deseq
updated 6.2 years ago by 43k • written 6.2 years ago by ▴ 10
5
votes
2
replies
1.6k
views
Is the VST implemented in DESeq useful on time-series cell differentiation datasets?
deseq deseq2 vst
updated 7.6 years ago by ★ 13k • written 7.6 years ago by • 0
5
votes
3
replies
7.5k
views
What problem does the MA plot diagnose? And how do you solve it?
deseq2 deseq rnaseq
updated 7.8 years ago by ★ 7.9k • written 7.8 years ago by ▴ 40
5
votes
13
replies
6.5k
views
P values from Deseq Analysis
deseq
7.6 years ago Shrikant Pawar • 0
4
votes
1
reply
14k
views
The latest version of R is 3.5.1 and it is not compatible with many Bioconductor packages.
R deseq tcgabiolinks
6.3 years ago ansari.sarabio • 0
4
votes
6
replies
1.8k
views
DESeq2 design and stats question
deseq2 differential binding analysis deseq atac-seq
updated 6.8 years ago by 43k • written 6.9 years ago by ▴ 60
4
votes
3
replies
2.8k
views
Why does Deseq, Deseq2, and EdgeR give vastly different results.
edger deseq deseq2
7.5 years ago michael.steffen ▴ 20
4
votes
2
replies
7.7k
views
Analyzing RNA-Seq data without replicates using DESeq
deseq DESeq2
updated 10.2 years ago by 43k • written 10.2 years ago by ▴ 90
4
votes
14
replies
20k
views
standard error value (lfcSE) returned by DeSeq2
deseq2 deseq lfc lfcse standard error
updated 7.7 years ago by • 0 • written 7.7 years ago by • 0
4
votes
6
replies
2.1k
views
Interpretation of DESeq2 results with 3 factorial design with interaction terms.
r DESeq DESeq2
3.2 years ago s-rhussien • 0
4
votes
4
replies
5.2k
views
TMM Normalization: DESeqDataSet: some values in assay are negative
deseq2 deseq normalization
updated 5.3 years ago by ▴ 40 • written 5.4 years ago by • 0
4
votes
7
replies
1.6k
views
Filtering DESeq2 result export along multiple lines
deseq2 differential binding analysis deseq
updated 7.0 years ago by 43k • written 7.0 years ago by ▴ 60
3
votes
4
replies
3.8k
views
Variance filtering prior to RNA-seq differential expression
sequencing deseq limma
updated 9.4 years ago by 52k • written 9.4 years ago by ▴ 420
3
votes
7
replies
1.4k
views
The discrepancy between the mean of extracted fitted value and calculated mean and SE based on LFC.
deseq2 deseq
6.3 years ago blastzone.heimerdinger ▴ 20
3
votes
5
replies
8.8k
views
DESeq2 resultsNames output
deseq deseq2
updated 9.8 years ago by 43k • written 9.8 years ago by ▴ 50
3
votes
7
replies
2.7k
views
novice: building gene co-expression network using RNA-Seq data
rna-seq WGCNA deseq method coexpression
updated 6.6 years ago by ★ 3.0k • written 6.6 years ago by ▴ 10
3
votes
3
replies
2.1k
views
read counts of paired end reads for DESeq2 analysis
deseq featurecounts paired
updated 8.6 years ago by ★ 13k • written 8.6 years ago by • 0
3
votes
14
replies
19k
views
Normalization in DESeq2
deseq2 deseq
updated 10.0 years ago by 43k • written 10.0 years ago by ▴ 90
3
votes
4
replies
3.1k
views
DESeq is better than DESeq2?
deseq2 deseq
8.7 years ago ribioinfo ▴ 100
3
votes
12
replies
1.9k
views
Why did I get NA p-values in DESeq with continuous variable?
deseq2 p-value continuous deseq
5.8 years ago ariel ▴ 20
3
votes
11
replies
3.9k
views
DESeq function taking too long
deseq2 deseq factor rnaseq
updated 7.4 years ago by ★ 3.0k • written 7.4 years ago by ▴ 30
3
votes
1
reply
6.4k
views
Deseq for pairwise comparison among many pairs
DESeq DESeq
updated 10.5 years ago by 43k • written 10.5 years ago by ▴ 20
3
votes
8
replies
4.8k
views
DESeq / DESeq2 for translation efficiency in polysome profiling or ribsome profiling experiments
Sequencing DESeq Sequencing DESeq
updated 8.3 years ago by • 0 • written 11.0 years ago by ★ 13k
3
votes
1
reply
1.4k
views
RNASeq testing for differential expression in one condition, equality in another (using DESeq)
deseq2 deseq rnaseq
7.8 years ago ysdel ▴ 40
3
votes
2
replies
13k
views
how to get normalized counts from edgeR
DESeq DESeq
updated 12.4 years ago by ▴ 880 • written 12.4 years ago by ★ 2.0k
3
votes
5
replies
2.7k
views
DESeq on transcripts v/s genes
DESeq DESeq
updated 12.8 years ago by ★ 13k • written 12.8 years ago by ▴ 410
3
votes
5
replies
2.8k
views
Using DESeq2: experimental design and extracting results
DESeq DESeq2 DESeq DESeq2
updated 10.5 years ago by 43k • written 10.5 years ago by ▴ 60
3
votes
2
replies
3.1k
views
Nanostring ncounterdata - DESeq
RNASeq Normalization Preprocessing DESeq RNASeq Normalization Preprocessing DESeq
updated 13.4 years ago by ★ 3.8k • written 13.4 years ago by ▴ 20
3
votes
5
replies
5.4k
views
Labeling points with hgnc symbols on the MA plot in DESeq2
deseq MA
updated 8.3 years ago by ▴ 150 • written 8.4 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: contrast matrix design for a continuous variable by dtzhu337 • 0
Thank you, Gordon. X is time splines for time point, and yes, it's needed. However, I was also thinking to incorporate time point with se…
Answer: contrast matrix design for a continuous variable by Gordon Smyth 52k
Yes, the design and contrasts are correct. Your analysis is also adjusted for covariates defined by X, which I assume is what you want to …
Comment: fail to use addPerROIQC in Rmd by liu.n • 0
That's odd. So it can run successfully within markdown but would be failed when knitting?
Comment: fail to use addPerROIQC in Rmd by joseph.joonsang • 0
> dim(spe) [1] 19962 425
Comment: fail to use addPerROIQC in Rmd by liu.n • 0
Hi, what's the output from `dim(spe)`?
Votes
Answer: contrast matrix design for a continuous variable
A: What's the difference between p.adjust and qvalue?
Answer: DESeq2- merging technical vs biological replicates
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: What type of counts data to import for performing Isoform analysis in edgeR
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