Showing : differential gene expression • reset
18
votes
37
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19k
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Correct construction of design matrix in limma for multiple contrasts for gene expression profiling
limma illumina differential gene expression multiple comparisons design matrix
10.6 years ago • updated 10.5 years ago svlachavas ▴ 840
6
votes
19
replies
5.3k
views
Time course analysis in DESeq2: handling common baseline for two experimental conditions
deseq2 timecourse multiple factor design RNAseq analysis differential gene expression
updated 8.3 years ago by ▴ 690 • written 8.3 years ago by ▴ 50
3
votes
19
replies
5.1k
views
remove batch effect and adjusted model for 4 covariates in Limma
limma batch effect covariates contrast differential gene expression
8.8 years ago mheydarpour ▴ 10
0
votes
19
replies
2.9k
views
Paired Difference Analysis
deseq2 R differential gene expression
8.4 years ago • updated 8.3 years ago nhua • 0
7
votes
18
replies
4.9k
views
RNA-seq analysis using EdgeR- I need to make sure that the codes that I use to analyze the data are correct
rnaseq edger differential gene expression
updated 9.8 years ago by ★ 7.9k • written 9.8 years ago by • 0
20
votes
18
replies
6.5k
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 10.3 years ago by ▴ 870 • written 10.3 years ago by ▴ 840
4
votes
17
replies
4.1k
views
Question about decideTests function and adj.p.value in "limma" R Package
limma r differential gene expression
updated 8.5 years ago by 53k • written 8.5 years ago by ▴ 120
14
votes
16
replies
3.7k
views
Limma - discrepancy in number of significant genes
limma differential gene expression microarray linear model
updated 10.6 years ago by 68k • written 10.6 years ago by ▴ 10
17
votes
14
replies
54k
views
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq differential gene expression logfc limma R
updated 3.6 years ago by • 0 • written 8.5 years ago by ▴ 20
5
votes
14
replies
7.6k
views
Possible ways to select differential expressed genes using DeSeq2 or edgeR
R deseq2 edger differential gene expression fold change
updated 3.7 years ago by ★ 5.0k • written 7.5 years ago by ▴ 60
10
votes
14
replies
15k
views
how DESeq calculates p-value ?
deseq differential gene expression statistics p-value
updated 4.9 years ago by ▴ 20 • written 9.9 years ago by ▴ 30
0
votes
13
replies
5.2k
views
DESeq2: collapseReplicates error
deseq2 rnaseq differential gene expression
9.4 years ago ta_awwad ▴ 10
3
votes
13
replies
3.2k
views
Design and independent filtering of patient RNA-seq data
differential gene expression deseq2 design independent filtering limma
updated 10.6 years ago by 68k • written 10.6 years ago by ▴ 110
6
votes
13
replies
4.4k
views
DEseq2 with limited gene set
DEseq2 differential gene expression
9.4 years ago dmr210 • 0
10
votes
13
replies
5.5k
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 10.5 years ago by • 0 • written 10.5 years ago by ▴ 10
1
vote
13
replies
3.5k
views
Why Differential expression results differ with edgeR and limma ?
limma edgeR differential gene expression r
8.4 years ago Biologist ▴ 120
3
votes
12
replies
28k
views
P Value of 0?
differential gene expression edger
updated 10.9 years ago by ▴ 180 • written 10.9 years ago by • 0
6
votes
12
replies
6.4k
views
DESEq2 - Why is "my gene" not differentially expressed?
deseq2 differential gene expression
9.8 years ago Jane Merlevede ▴ 90
5
votes
12
replies
10k
views
Filtering step for differential analysis in edgeR
r edger differential gene expression filtering bioconductor
updated 7.7 years ago by 53k • written 7.7 years ago by ▴ 120
6
votes
12
replies
20k
views
Problem making DESeq dataset; Error all variables in design formula must be columns in colData
deseq2 deseq counts rnaseq differential gene expression
updated 9.7 years ago by 43k • written 9.7 years ago by ▴ 10
5
votes
12
replies
6.4k
views
Differential expression analysis: comparison of DESeq2 and edgeR robust results
deseq2 edgeR differential gene expression
updated 9.7 years ago by ★ 29k • written 9.7 years ago by ▴ 90
1
vote
10
replies
6.8k
views
DESEQ2: apparently wrong log2(fold-change) calculation
deseq2 differential gene expression log2fc
9.8 years ago Osvaldo ▴ 40
6
votes
10
replies
2.6k
views
Possible implementation of roast/mroast for testing common DE patterns across two different experiments
gene set testing roast mroast differential gene expression bioconductor
10.7 years ago svlachavas ▴ 840
9
votes
10
replies
5.9k
views
Simple significance test functions from R packages limma and plsgenomics
limma plsgenomics microarray differential gene expression
updated 11.0 years ago by 53k • written 11.0 years ago by ▴ 10
5
votes
9
replies
4.3k
views
Merge different datasets regarding a common number of DE genes in R
bioconductor expresiondataset affymetrixchip differential gene expression
10.9 years ago • updated 10.8 years ago svlachavas ▴ 840
2
votes
9
replies
2.1k
views
SNP-level Allele-specific expression detection using DESeq2 in an unpaired experimental design
deseq2 rnaseq differential gene expression
8.2 years ago • updated 8.1 years ago engelbrecht.stephan ▴ 10
7
votes
9
replies
6.3k
views
LIMMA: interpreting interaction terms in an unbalanced factorial design with repeated measures
LIMMA FACTORIAL REPEATED MEASURES differential gene expression
10.4 years ago • updated 10.2 years ago robert.maughan • 0
1
vote
9
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2.4k
views
edgeR in a situation with unbalanced design: to include only subjects with matching time points or not?
edgeR differential gene expression
updated 8.4 years ago by 53k • written 8.5 years ago by ▴ 20
5
votes
9
replies
7.2k
views
how to control age and gender effect in expression data using DESeq2
deseq2 rnaseq mirna-seq differential gene expression
written 7.9 years ago by ▴ 20
2
votes
9
replies
2.5k
views
Loads, really loads of DEGs after edgeR differential analysis
rnaseq edger normalization differential gene expression
8.1 years ago David R ▴ 90
0
votes
9
replies
2.4k
views
DESeq2 influence of 2 samples
deseq2 outliers differential gene expression
updated 8.9 years ago by 43k • written 8.9 years ago by ▴ 10
2
votes
9
replies
2.5k
views
decideTests error with edgeR package
edger r differential gene expression
updated 8.4 years ago by ★ 29k • written 8.4 years ago by ▴ 120
11
votes
8
replies
13k
views
Limma and batch effect
limma differential gene expression clustering removebatcheffect
updated 8.3 years ago by 53k • written 8.3 years ago by ▴ 80
8
votes
8
replies
2.8k
views
Confounded design, batch effect correction (edgeR)
rnaseq edger differential gene expression batch effect
written 7.3 years ago by ▴ 20
0
votes
8
replies
3.6k
views
Problems with LRT code using DESeq2
deseq2 LRT differential gene expression
10.1 years ago • updated 10.0 years ago newsomew13 • 0
2
votes
8
replies
5.5k
views
MDS Plot help in edgeR
edgeR plotmds differential gene expression MDS mdsplot
updated 7.0 years ago by 53k • written 7.0 years ago by • 0
7
votes
8
replies
7.0k
views
Only one replicate: inferring dispersion from other group
deseq2 edger limma differential gene expression
updated 11.1 years ago by 53k • written 11.1 years ago by ▴ 30
1
vote
8
replies
4.1k
views
[DESeq2] Automatic outlier detection and replacement with continuous variables
deseq2 outliers RNAseq differential gene expression
8.8 years ago cajawe • 0
3
votes
8
replies
3.3k
views
EdgeR for differential analysis between two cell lines without replication
edger differential gene expression rnaseq
updated 7.5 years ago by 53k • written 7.5 years ago by ▴ 120
0
votes
8
replies
2.3k
views
DESeq2 glibc error
deseq2 differential gene expression model matrix
updated 8.9 years ago by 43k • written 8.9 years ago by ▴ 10
4
votes
8
replies
3.4k
views
Can't find any differentially expressed genes
rnaseq differential gene expression design matrix edgeR
updated 10.8 years ago by 53k • written 10.8 years ago by ▴ 10
0
votes
8
replies
6.7k
views
Comparing between two differential expression analysis - two different fold changes
Deseq deseq2 differential gene expression rnaseq statistical test
7.9 years ago Marina ▴ 40
0
votes
7
replies
5.9k
views
Visualization of rownames in the heatmap.2 function for selected DE genes of a microarray dataset
heatmap.2 gplots differential gene expression visualization
10.8 years ago svlachavas ▴ 840
1
vote
7
replies
7.3k
views
featureCounts creating fragments and high NoFeatures value
featurecounts bioconductor differential gene expression star
updated 9.0 years ago by ★ 3.6k • written 9.0 years ago by ▴ 10
1
vote
7
replies
3.0k
views
CellCODE not installing
differential gene expression microarray
9.8 years ago christopher.clarskon15 ▴ 20
4
votes
7
replies
3.6k
views
Can we use glmQLFit instead of glmFit and then glmLRT in edgeR
edger differential gene expression glmlrt()
9.1 years ago simarsidhu25 • 0
1
vote
7
replies
2.4k
views
DESeq2: use of unmix() function for deconvolution of whole blood
deseq2 bioconductor rnaseq differential gene expression
updated 8.7 years ago by 43k • written 8.7 years ago by • 0
0
votes
7
replies
2.7k
views
DESeq2 with interest only for 1 gene
R deseq2 differential gene expression help
9.6 years ago fischer87 • 0
4
votes
7
replies
2.4k
views
assigning differential exons to trascripts
dexseq rsem differential exon usage differential gene expression
updated 9.5 years ago by 68k • written 9.5 years ago by ★ 1.5k
0
votes
7
replies
4.9k
views
Deciding on cooks cutoff value DESeq2
deseq2 differential gene expression outliers bioconductor
updated 9.0 years ago by 43k • written 9.0 years ago by ▴ 10
272 results • Page 1 of 6
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Replies
Answer: Confounded design, batch effect correction (edgeR) by nig.httopss • 0
To perform gene matching accurately, you should use the formula ~0 + Group + Batch in the design matrix to better manage sample groups. Sin…
Comment: Clarification on counting in Rsubread (featureCounts) by Gordon Smyth 53k
Have you told featureCounts to do strand-specific counting? As pointed out by Frances Turner, you can lose reads if they overlap the gene …
Answer: Clarification on counting in Rsubread (featureCounts) by Frances Turner ▴ 10
You should look at the summary files produced by feature counts. This gives a breakdown of what happened to reads that were not assigned. Y…
Comment: Incosistencies in buildSNNGraph() function by ATpoint ★ 5.0k
Just played with this a bit and I think it comes down to not having a fixed seed before running the leiden thingy. Same goes for PCA and UM…
Answer: Incosistencies in buildSNNGraph() function by Aaron Lun ★ 29k
The most obvious thing that comes to mind is the RNG seed. `cluster_leiden()` does some random number generation, somewhere deep in the **i…
Votes
Answer: Clarification on counting in Rsubread (featureCounts)
C: RNA-Seq analysis with Limma/edgeR, time course experiment, aberrant results
C: RNA-Seq analysis with Limma/edgeR, time course experiment, aberrant results
A: Conversion from counts to FPKM
Answer: Incosistencies in buildSNNGraph() function
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