Showing : differential gene expression • reset
0
votes
3
replies
1.9k
views
Calculating a score from fold change matrix of pair-wise rna-seq data
rna-seq deseq2 differential gene expression biostatistics
9.5 years ago g.atla ▴ 10
1
vote
10
replies
6.6k
views
DESEQ2: apparently wrong log2(fold-change) calculation
deseq2 differential gene expression log2fc
9.5 years ago Osvaldo ▴ 40
1
vote
7
replies
2.9k
views
CellCODE not installing
differential gene expression microarray
9.5 years ago christopher.clarskon15 ▴ 20
0
votes
1
reply
898
views
Identify genes of changed expression using R
differential gene expression r commander
updated 9.6 years ago by ★ 29k • written 9.6 years ago by • 0
6
votes
12
replies
6.2k
views
DESEq2 - Why is "my gene" not differentially expressed?
deseq2 differential gene expression
9.6 years ago Jane Merlevede ▴ 90
1
vote
3
replies
1.2k
views
Grouping similar genes in differential expression analysis to increase power
deseq2 rnaseq differential gene expression
updated 9.6 years ago by 43k • written 9.6 years ago by • 0
10
votes
14
replies
15k
views
how DESeq calculates p-value ?
deseq differential gene expression statistics p-value
updated 4.6 years ago by ▴ 20 • written 9.6 years ago by ▴ 30
4
votes
7
replies
1.6k
views
off-target effects in DE analysis
edger differential gene expression
updated 9.7 years ago by ★ 29k • written 9.7 years ago by ▴ 10
2
votes
1
reply
1.8k
views
no DGE with multiple groups in edge R
edgeR differential gene expression RNAseq
updated 9.7 years ago by ★ 29k • written 9.7 years ago by ▴ 20
4
votes
4
replies
1.8k
views
Setting contrasts in limma where null hypothesis is that Test = 2 x Control
differential gene expression limma rnaseq design and contrast matrix limma voom
9.7 years ago stuart ▴ 10
0
votes
0
replies
2.0k
views
limma: blocking factors and factorial design
limma differential gene expression design and contrast matrix covariates
9.7 years ago jlerga • 0
5
votes
1
reply
2.3k
views
WGCNA - looking for over-representation of DEGs within gene networks
wgcna r differential gene expression bioconductor
updated 9.7 years ago by ★ 3.0k • written 9.7 years ago by ▴ 30
0
votes
3
replies
1.4k
views
detect cancer in some tissue
cancer differential gene expression
updated 9.7 years ago by ▴ 10 • written 9.9 years ago by • 0
5
votes
6
replies
4.0k
views
Differential expression analysis - additive genetic model (how to implement it)
deseq2 edger differential gene expression additive model
9.8 years ago • updated 9.7 years ago jlerga • 0
0
votes
8
replies
3.5k
views
Problems with LRT code using DESeq2
deseq2 LRT differential gene expression
9.9 years ago • updated 9.7 years ago newsomew13 • 0
2
votes
3
replies
2.2k
views
Getting up/down regulation info on DEG using edgeR
edger differential gene expression
updated 9.7 years ago by ★ 13k • written 9.8 years ago by • 0
3
votes
5
replies
2.5k
views
How to handle mix of samples from the same subject and from different subjects during differential expression analysis of RNA-seq using GLMs?
rnaseq rna-seq differential gene expression differential expression edger
updated 9.8 years ago by ★ 7.9k • written 9.8 years ago by ▴ 70
2
votes
4
replies
1.5k
views
convert a character vector into a numeric vector
differential gene expression
updated 9.8 years ago by ★ 29k • written 9.8 years ago by • 0
0
votes
2
replies
3.3k
views
DESeq2 different results from similar datasets
deseq2 differential gene expression rna-seq
9.8 years ago erin.gill81 ▴ 60
1
vote
2
replies
2.9k
views
DESeq2 -- Comparing factors while fixing another factor
deseq2 differential gene expression multiple factor design
updated 9.9 years ago by 43k • written 9.9 years ago by ▴ 30
0
votes
7
replies
2.8k
views
ExpressionSet expression values is negative from NCBI GSE data set
microarray differential gene expression
updated 9.9 years ago by 53k • written 9.9 years ago by ▴ 60
1
vote
1
reply
4.0k
views
Ideal Statistical Analysis for FPKM Gene Expression Data Generated by RSEM
differential gene expression
updated 9.9 years ago by ★ 29k • written 9.9 years ago by • 0
0
votes
1
reply
1.8k
views
HTA analysis at transcript level
pd.hta.2.0 transcript differential gene expression
updated 9.9 years ago by 68k • written 9.9 years ago by ▴ 40
1
vote
5
replies
4.1k
views
Contrast All Interaction Effects in DESeq2 in current version (1.10.1)
DESeq2 differential gene expression interactions
9.9 years ago marcus.stoiber • 0
7
votes
9
replies
6.1k
views
LIMMA: interpreting interaction terms in an unbalanced factorial design with repeated measures
LIMMA FACTORIAL REPEATED MEASURES differential gene expression
10.1 years ago • updated 9.9 years ago robert.maughan • 0
1
vote
4
replies
1.7k
views
Specificity of gene expression
differential gene expression specific expression contrast deseq2
10.0 years ago arrigonialberto86 • 0
2
votes
1
reply
2.4k
views
differential expressed genes, paired samples and multiple factors
edgeR batch effect differential gene expression paired samples
updated 10.0 years ago by ★ 29k • written 10.0 years ago by ▴ 10
4
votes
6
replies
7.1k
views
Using RPKM data in bioconductor for gene expression analysis
rpkm/fpkm differential gene expression
updated 10.0 years ago by 68k • written 10.0 years ago by ▴ 110
1
vote
2
replies
1.5k
views
Deseq2 analysis with replicates only for control
deseq2 differential gene expression
updated 10.0 years ago by 43k • written 10.0 years ago by ▴ 20
20
votes
18
replies
6.2k
views
Using of limma moderated t-test with "corrected" expression matrix resulting from ComBat batch effect correction
limma batch effect ComBat differential gene expression
updated 10.0 years ago by ▴ 870 • written 10.0 years ago by ▴ 840
1
vote
0
replies
1.9k
views
Job: PhD Student in Computational Biology
differential gene expression rnaseq riboseqr computational biology Job
10.0 years ago Bernd Fischer ▴ 550
1
vote
6
replies
1.7k
views
Intronic sequences are the majority of the top differentially expressed genes
limma microarray normalization oligo differential gene expression
updated 10.1 years ago by 68k • written 10.1 years ago by • 0
0
votes
0
replies
1.5k
views
RankProd: simultaneously up and down regulated gene
RankProd differential gene expression
10.1 years ago horcsct ▴ 10
3
votes
6
replies
3.0k
views
How to get a list of differentialy expressed genes with data from Illumina array?
limma illumina microarray lmfit differential gene expression
updated 10.2 years ago by 68k • written 10.2 years ago by ▴ 10
1
vote
4
replies
4.9k
views
Running DESeqDataSet with 4 factors?
summarizedexperiment deseq2 deseqdataset multiple factor design differential gene expression
10.2 years ago Lillyhchen ▴ 10
18
votes
37
replies
18k
views
Correct construction of design matrix in limma for multiple contrasts for gene expression profiling
limma illumina differential gene expression multiple comparisons design matrix
10.3 years ago • updated 10.2 years ago svlachavas ▴ 840
8
votes
2
replies
3.0k
views
limma-voom when testing differential expression of a subset of genes.
limma voom differential gene expression
updated 10.2 years ago by 53k • written 10.2 years ago by ▴ 40
0
votes
2
replies
1.8k
views
Diffrential expression analysis of human vs. mouse
deseq2 cuffdiff differential gene expression
10.2 years ago Assa Yeroslaviz ★ 1.5k
6
votes
4
replies
4.5k
views
Merge different datasets and perform differential expression analysis in limma
insilicomerging batcheffect limma differential gene expression bioconductor
updated 10.2 years ago by ★ 29k • written 10.2 years ago by ▴ 840
10
votes
13
replies
5.2k
views
Trouble identifying differentially expressed genes on Affymetrix Human Gene 2.0.ST using R with oligo and limma package
R limma oligo differential gene expression affymetrix microarrays
updated 10.3 years ago by • 0 • written 10.3 years ago by ▴ 10
1
vote
1
reply
1.1k
views
Best formula to use for this experimental setup
deseq2 differential gene expression design
updated 10.3 years ago by 43k • written 10.3 years ago by • 0
14
votes
16
replies
3.5k
views
Limma - discrepancy in number of significant genes
limma differential gene expression microarray linear model
updated 10.3 years ago by 68k • written 10.3 years ago by ▴ 10
3
votes
13
replies
3.0k
views
Design and independent filtering of patient RNA-seq data
differential gene expression deseq2 design independent filtering limma
updated 10.3 years ago by 68k • written 10.3 years ago by ▴ 110
0
votes
3
replies
1.4k
views
Differential Expression using simpleaffy R package
r differential gene expression
updated 10.4 years ago by 68k • written 10.4 years ago by ▴ 260
6
votes
10
replies
2.4k
views
Possible implementation of roast/mroast for testing common DE patterns across two different experiments
gene set testing roast mroast differential gene expression bioconductor
10.4 years ago svlachavas ▴ 840
0
votes
1
reply
944
views
Find differentially expressed values
differential gene expression differential expression edgeR
updated 10.4 years ago by 53k • written 10.4 years ago by • 0
1
vote
2
replies
1.9k
views
Question about read.maimages
differential gene expression limma read.maimages
updated 10.4 years ago by 53k • written 10.4 years ago by ▴ 10
1
vote
3
replies
3.6k
views
DESeq2 effects of treatment at different time points including subject ID
deseq2 rnaseq differential gene expression
10.4 years ago Catalina Aguilar Hurtado ▴ 90
2
votes
2
replies
1.2k
views
factorial linear modeling from DEseq2
deseq2 rnaseq differential gene expression
updated 10.4 years ago by ★ 13k • written 10.4 years ago by • 0
4
votes
8
replies
3.4k
views
Can't find any differentially expressed genes
rnaseq differential gene expression design matrix edgeR
updated 10.5 years ago by 53k • written 10.5 years ago by ▴ 10
272 results • Page 5 of 6
Recent ...
Replies
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 4.9k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 4.9k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Comment: R course in Boston December 19-20 by eja.gaasa2e.r.m • 0
The upcoming XLSolutions R course in Boston on December 19 20 is a great opportunity to enhance your data skills. Whether you re a beginner…
Answer: Gatins Set error by James W. MacDonald 68k
`GatingSet` isn't a function in `flowCore`. It is however in `flowWorkspace`, which you would need to load first.
Answer: How to model DE for RNA-seq in concordant monozygotic twins? by Gordon Smyth 53k
Your question is more about science than it is about software syntax, and I can't give advice about how to conduct a scientific analysis, n…
Votes
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
Answer: ordinary t from limma [was: How would I normally compare swirl?]
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Awards • All
Popular Question to Gordon Smyth 53k
Popular Question to shepherl 4.2k
Popular Question to Joseph • 0
Popular Question to zhe ▴ 20
Popular Question to Natalia • 0
Locations • All
United States, 4 hours ago
The city by the bay, 4 hours ago
United States, 6 hours ago
Seattle, WA, United States, 12 hours ago
Pittsburgh, United States, 12 hours ago
Traffic: 668 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6