Showing : differential gene expression • reset
18
votes
37
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18k
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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
9.8 years ago • updated 9.7 years ago svlachavas ▴ 840
3
votes
19
replies
4.4k
views
remove batch effect and adjusted model for 4 covariates in Limma
limma batch effect covariates contrast differential gene expression
8.0 years ago mheydarpour ▴ 10
0
votes
19
replies
2.4k
views
Paired Difference Analysis
deseq2 R differential gene expression
7.6 years ago • updated 7.5 years ago nhua • 0
6
votes
19
replies
4.5k
views
Time course analysis in DESeq2: handling common baseline for two experimental conditions
deseq2 timecourse multiple factor design RNAseq analysis differential gene expression
updated 7.5 years ago by ▴ 690 • written 7.5 years ago by ▴ 50
20
votes
18
replies
5.6k
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 9.5 years ago by ▴ 870 • written 9.5 years ago by ▴ 840
7
votes
18
replies
4.3k
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 9.0 years ago by ★ 7.9k • written 9.0 years ago by • 0
4
votes
17
replies
3.4k
views
Question about decideTests function and adj.p.value in "limma" R Package
limma r differential gene expression
updated 7.7 years ago by 52k • written 7.7 years ago by ▴ 120
14
votes
16
replies
3.2k
views
Limma - discrepancy in number of significant genes
limma differential gene expression microarray linear model
updated 9.7 years ago by 68k • written 9.7 years ago by ▴ 10
5
votes
14
replies
6.2k
views
Possible ways to select differential expressed genes using DeSeq2 or edgeR
R deseq2 edger differential gene expression fold change
updated 2.9 years ago by ★ 4.7k • written 6.7 years ago by ▴ 60
10
votes
14
replies
14k
views
how DESeq calculates p-value ?
deseq differential gene expression statistics p-value
updated 4.0 years ago by ▴ 20 • written 9.1 years ago by ▴ 30
17
votes
14
replies
49k
views
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq differential gene expression logfc limma R
updated 2.7 years ago by • 0 • written 7.7 years ago by ▴ 20
6
votes
13
replies
3.8k
views
DEseq2 with limited gene set
DEseq2 differential gene expression
8.6 years ago dmr210 • 0
0
votes
13
replies
4.7k
views
DESeq2: collapseReplicates error
deseq2 rnaseq differential gene expression
8.6 years ago • updated 8.5 years ago ta_awwad ▴ 10
3
votes
13
replies
2.7k
views
Design and independent filtering of patient RNA-seq data
differential gene expression deseq2 design independent filtering limma
updated 9.8 years ago by 68k • written 9.8 years ago by ▴ 110
10
votes
13
replies
5.0k
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 9.7 years ago by • 0 • written 9.7 years ago by ▴ 10
1
vote
13
replies
3.0k
views
Why Differential expression results differ with edgeR and limma ?
limma edgeR differential gene expression r
7.6 years ago Biologist ▴ 120
3
votes
12
replies
26k
views
P Value of 0?
differential gene expression edger
updated 10.1 years ago by ▴ 180 • written 10.1 years ago by • 0
6
votes
12
replies
5.8k
views
DESEq2 - Why is "my gene" not differentially expressed?
deseq2 differential gene expression
9.0 years ago Jane Merlevede ▴ 90
5
votes
12
replies
8.3k
views
Filtering step for differential analysis in edgeR
r edger differential gene expression filtering bioconductor
updated 6.9 years ago by 52k • written 6.9 years ago by ▴ 120
6
votes
12
replies
19k
views
Problem making DESeq dataset; Error all variables in design formula must be columns in colData
deseq2 deseq counts rnaseq differential gene expression
updated 8.9 years ago by 43k • written 8.9 years ago by ▴ 10
5
votes
12
replies
5.7k
views
Differential expression analysis: comparison of DESeq2 and edgeR robust results
deseq2 edgeR differential gene expression
updated 8.8 years ago by ★ 28k • written 8.8 years ago by ▴ 90
1
vote
10
replies
6.4k
views
DESEQ2: apparently wrong log2(fold-change) calculation
deseq2 differential gene expression log2fc
9.0 years ago Osvaldo ▴ 40
6
votes
10
replies
2.2k
views
Possible implementation of roast/mroast for testing common DE patterns across two different experiments
gene set testing roast mroast differential gene expression bioconductor
9.9 years ago • updated 9.8 years ago svlachavas ▴ 840
9
votes
10
replies
5.5k
views
Simple significance test functions from R packages limma and plsgenomics
limma plsgenomics microarray differential gene expression
updated 10.2 years ago by 52k • written 10.2 years ago by ▴ 10
5
votes
9
replies
3.7k
views
Merge different datasets regarding a common number of DE genes in R
bioconductor expresiondataset affymetrixchip differential gene expression
10.0 years ago svlachavas ▴ 840
2
votes
9
replies
1.7k
views
SNP-level Allele-specific expression detection using DESeq2 in an unpaired experimental design
deseq2 rnaseq differential gene expression
7.4 years ago • updated 7.3 years ago engelbrecht.stephan ▴ 10
7
votes
9
replies
5.7k
views
LIMMA: interpreting interaction terms in an unbalanced factorial design with repeated measures
LIMMA FACTORIAL REPEATED MEASURES differential gene expression
9.6 years ago • updated 9.4 years ago robert.maughan • 0
1
vote
9
replies
2.2k
views
edgeR in a situation with unbalanced design: to include only subjects with matching time points or not?
edgeR differential gene expression
updated 7.6 years ago by 52k • written 7.6 years ago by ▴ 20
2
votes
9
replies
6.5k
views
how to control age and gender effect in expression data using DESeq2
deseq2 rnaseq mirna-seq differential gene expression
written 7.0 years ago by ▴ 10
2
votes
9
replies
2.1k
views
Loads, really loads of DEGs after edgeR differential analysis
rnaseq edger normalization differential gene expression
7.3 years ago David R ▴ 90
0
votes
9
replies
2.0k
views
DESeq2 influence of 2 samples
deseq2 outliers differential gene expression
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 10
2
votes
9
replies
2.1k
views
decideTests error with edgeR package
edger r differential gene expression
updated 7.6 years ago by ★ 28k • written 7.6 years ago by ▴ 120
2
votes
8
replies
4.9k
views
MDS Plot help in edgeR
edgeR plotmds differential gene expression MDS mdsplot
updated 6.2 years ago by 52k • written 6.2 years ago by • 0
0
votes
8
replies
3.3k
views
Problems with LRT code using DESeq2
deseq2 LRT differential gene expression
9.3 years ago • updated 9.2 years ago newsomew13 • 0
11
votes
8
replies
12k
views
Limma and batch effect
limma differential gene expression clustering removebatcheffect
updated 7.5 years ago by 52k • written 7.5 years ago by ▴ 80
7
votes
8
replies
6.3k
views
Only one replicate: inferring dispersion from other group
deseq2 edger limma differential gene expression
updated 10.3 years ago by 52k • written 10.3 years ago by ▴ 30
1
vote
8
replies
3.6k
views
[DESeq2] Automatic outlier detection and replacement with continuous variables
deseq2 outliers RNAseq differential gene expression
8.0 years ago cajawe • 0
3
votes
8
replies
3.0k
views
EdgeR for differential analysis between two cell lines without replication
edger differential gene expression rnaseq
updated 6.7 years ago by 52k • written 6.7 years ago by ▴ 120
0
votes
8
replies
2.1k
views
DESeq2 glibc error
deseq2 differential gene expression model matrix
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 10
4
votes
8
replies
3.1k
views
Can't find any differentially expressed genes
rnaseq differential gene expression design matrix edgeR
updated 9.9 years ago by 52k • written 10.0 years ago by ▴ 10
0
votes
8
replies
6.0k
views
Comparing between two differential expression analysis - two different fold changes
Deseq deseq2 differential gene expression rnaseq statistical test
7.1 years ago Marina ▴ 40
0
votes
7
replies
5.5k
views
Visualization of rownames in the heatmap.2 function for selected DE genes of a microarray dataset
heatmap.2 gplots differential gene expression visualization
10.0 years ago svlachavas ▴ 840
1
vote
7
replies
6.4k
views
featureCounts creating fragments and high NoFeatures value
featurecounts bioconductor differential gene expression star
updated 8.1 years ago by ★ 3.6k • written 8.1 years ago by ▴ 10
1
vote
7
replies
2.7k
views
CellCODE not installing
differential gene expression microarray
9.0 years ago christopher.clarskon15 ▴ 20
4
votes
7
replies
3.3k
views
Can we use glmQLFit instead of glmFit and then glmLRT in edgeR
edger differential gene expression glmlrt()
8.3 years ago simarsidhu25 • 0
1
vote
7
replies
2.2k
views
DESeq2: use of unmix() function for deconvolution of whole blood
deseq2 bioconductor rnaseq differential gene expression
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
0
votes
7
replies
2.4k
views
DESeq2 with interest only for 1 gene
R deseq2 differential gene expression help
8.8 years ago • updated 8.7 years ago fischer87 • 0
4
votes
7
replies
2.0k
views
assigning differential exons to trascripts
dexseq rsem differential exon usage differential gene expression
updated 8.7 years ago by 68k • written 8.7 years ago by ★ 1.5k
0
votes
7
replies
4.4k
views
Deciding on cooks cutoff value DESeq2
deseq2 differential gene expression outliers bioconductor
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 10
1
vote
7
replies
1.8k
views
Strange distribution of logFC
edger deseq2 rnaseq differential gene expression
updated 7.4 years ago by ★ 28k • written 7.4 years ago by ▴ 20
50 results • Page 1 of 1
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Comment: DiffBind custom normalization factor by Abbie • 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2? by James W. MacDonald 68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore by Michael Love 43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi by Michael Love 43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
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