Showing : differential gene expression • reset
18
votes
18
replies
4.8k
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 8.6 years ago by ▴ 850 • written 8.6 years ago by ▴ 830
18
votes
37
replies
17k
views
Correct construction of design matrix in limma for multiple contrasts for gene expression profiling
limma illumina differential gene expression multiple comparisons design matrix
8.9 years ago • updated 8.8 years ago svlachavas ▴ 830
17
votes
14
replies
40k
views
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq differential gene expression logfc limma R
updated 22 months ago by • 0 • written 6.8 years ago by ▴ 20
14
votes
16
replies
2.6k
views
Limma - discrepancy in number of significant genes
limma differential gene expression microarray linear model
updated 8.9 years ago by 65k • written 8.9 years ago by ▴ 10
12
votes
6
replies
1.6k
views
Testing for DE genes
affymetrix microarrays limma differential gene expression
updated 7.0 years ago by ★ 28k • written 7.0 years ago by ▴ 10
12
votes
6
replies
2.6k
views
How did the edgeR authors compute Figure 2 (genewise deviance statistics?)
edger differential gene expression rnaseq
updated 7.1 years ago by 50k • written 7.1 years ago by ▴ 20
11
votes
8
replies
10k
views
Limma and batch effect
limma differential gene expression clustering removebatcheffect
updated 6.7 years ago by 50k • written 6.7 years ago by ▴ 80
10
votes
4
replies
4.4k
views
Filtering lowly expressed genes in voom-limma analysis
voom limma rna-seq differential gene expression
updated 7.8 years ago by 50k • written 7.8 years ago by ▴ 110
10
votes
14
replies
13k
views
how DESeq calculates p-value ?
deseq differential gene expression statistics p-value
updated 3.2 years ago by ▴ 20 • written 8.2 years ago by ▴ 30
10
votes
13
replies
4.3k
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 8.8 years ago by • 0 • written 8.9 years ago by ▴ 10
9
votes
5
replies
4.3k
views
Finding DE genes from RNA-seq data
edgeR pvalue qvalue fpkm differential gene expression
updated 5.5 years ago by ★ 13k • written 5.5 years ago by • 0
9
votes
10
replies
4.9k
views
Simple significance test functions from R packages limma and plsgenomics
limma plsgenomics microarray differential gene expression
updated 9.3 years ago by 50k • written 9.3 years ago by ▴ 10
8
votes
2
replies
2.5k
views
limma-voom when testing differential expression of a subset of genes.
limma voom differential gene expression
updated 8.8 years ago by 50k • written 8.8 years ago by ▴ 40
8
votes
7
replies
1.9k
views
Confounded design, batch effect correction (edgeR)
rnaseq edger differential gene expression batch effect
updated 4.9 years ago by • 0 • written 5.7 years ago by ▴ 20
7
votes
9
replies
5.0k
views
LIMMA: interpreting interaction terms in an unbalanced factorial design with repeated measures
LIMMA FACTORIAL REPEATED MEASURES differential gene expression
8.7 years ago • updated 8.5 years ago robert.maughan • 0
7
votes
8
replies
5.3k
views
Only one replicate: inferring dispersion from other group
deseq2 edger limma differential gene expression
updated 9.4 years ago by 50k • written 9.4 years ago by ▴ 30
7
votes
18
replies
3.7k
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 8.1 years ago by ★ 7.9k • written 8.1 years ago by • 0
7
votes
6
replies
5.8k
views
scaling data for clustering heat map
edger heatmap clustering differential gene expression rnaseq
updated 5.9 years ago by 50k • written 5.9 years ago by ▴ 60
7
votes
7
replies
3.1k
views
Using Sailfish estimated read-counts for DESeq2 analysis
deseq2 sailfish differential gene expression
updated 9.5 years ago by ★ 3.7k • written 9.5 years ago by • 0
6
votes
4
replies
4.0k
views
Merge different datasets and perform differential expression analysis in limma
insilicomerging batcheffect limma differential gene expression bioconductor
updated 8.8 years ago by ★ 28k • written 8.8 years ago by ▴ 830
6
votes
19
replies
3.6k
views
Time course analysis in DESeq2: handling common baseline for two experimental conditions
deseq2 timecourse multiple factor design RNAseq analysis differential gene expression
updated 6.6 years ago by ▴ 680 • written 6.6 years ago by ▴ 50
6
votes
12
replies
17k
views
Problem making DESeq dataset; Error all variables in design formula must be columns in colData
deseq2 deseq counts rnaseq differential gene expression
updated 8.0 years ago by 42k • written 8.0 years ago by ▴ 10
6
votes
7
replies
2.2k
views
Multi-level experiment with limma
limma design and contrast matrix differential gene expression regression
updated 6.8 years ago by ★ 28k • written 6.8 years ago by • 0
6
votes
13
replies
3.0k
views
DEseq2 with limited gene set
DEseq2 differential gene expression
7.7 years ago dmr210 • 0
6
votes
10
replies
1.8k
views
Possible implementation of roast/mroast for testing common DE patterns across two different experiments
gene set testing roast mroast differential gene expression bioconductor
9.0 years ago svlachavas ▴ 830
6
votes
12
replies
5.1k
views
DESEq2 - Why is "my gene" not differentially expressed?
deseq2 differential gene expression
8.2 years ago Jane Merlevede ▴ 90
5
votes
6
replies
3.2k
views
Differential expression analysis - additive genetic model (how to implement it)
deseq2 edger differential gene expression additive model
8.4 years ago • updated 8.3 years ago jlerga • 0
5
votes
9
replies
3.1k
views
Merge different datasets regarding a common number of DE genes in R
bioconductor expresiondataset affymetrixchip differential gene expression
9.2 years ago svlachavas ▴ 830
5
votes
2
replies
4.0k
views
deseq2 LRT vs Wald test results for DE expression among 4 conditions
rnaseq deseq2 lrt wald differential gene expression
updated 2.1 years ago by • 0 • written 6.7 years ago by • 0
5
votes
4
replies
1.6k
views
How to remove dublicate probesets matching to the same gene, after toptable in order to have a genelist without dublicate gene Symbols for further GO…
bioconductor limma differential gene expression dublicate
9.2 years ago svlachavas ▴ 830
5
votes
6
replies
1.6k
views
How to set up appropriate analysis using sample type and condition for DESeq2
deseq2 differential gene expression design
updated 5.6 years ago by 42k • written 5.6 years ago by • 0
5
votes
6
replies
1.4k
views
Confusing: identify differentially expression genes (DEG) perturbed by a drug in Limma
limma cmap microarrays differential gene expression
7.3 years ago kevin.m.hao ▴ 10
5
votes
14
replies
4.9k
views
Possible ways to select differential expressed genes using DeSeq2 or edgeR
R deseq2 edger differential gene expression fold change
updated 2.0 years ago by ★ 4.1k • written 5.8 years ago by ▴ 60
5
votes
12
replies
6.5k
views
Filtering step for differential analysis in edgeR
r edger differential gene expression filtering bioconductor
updated 6.0 years ago by 50k • written 6.0 years ago by ▴ 110
5
votes
4
replies
2.7k
views
Why DESeq2 and edgeR give different results?
deseq2 rnaseq differential gene expression edger
updated 2.9 years ago by 50k • written 6.0 years ago by ▴ 110
5
votes
1
reply
1.8k
views
WGCNA - looking for over-representation of DEGs within gene networks
wgcna r differential gene expression bioconductor
updated 8.3 years ago by ★ 3.0k • written 8.3 years ago by ▴ 30
5
votes
12
replies
4.7k
views
Differential expression analysis: comparison of DESeq2 and edgeR robust results
deseq2 edgeR differential gene expression
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 90
5
votes
5
replies
2.3k
views
Performing differential gene analysis on RT PCR experimental data
differential gene expression
updated 6.3 years ago by 50k • written 6.3 years ago by ▴ 10
5
votes
3
replies
1.4k
views
Setting gene expression thresholds for trajectory analysis using Monocle
monocle differential gene expression detectgenes function Tutorial
5.3 years ago S.Webb6 ▴ 40
4
votes
6
replies
3.1k
views
edgeR on DEG analysis: Size cannot be NA nor exceed 65536
edger differential gene expression
updated 7.2 years ago by 65k • written 7.2 years ago by • 0
4
votes
4
replies
1.7k
views
edgeR: How can I determine which factors significantly explain my DE genes?
edger differential gene expression model.matrix design matrix
updated 6.0 years ago by 50k • written 6.0 years ago by • 0
4
votes
7
replies
1.7k
views
assigning differential exons to trascripts
dexseq rsem differential exon usage differential gene expression
updated 7.9 years ago by 65k • written 7.9 years ago by ★ 1.5k
4
votes
2
replies
1.2k
views
Differential gene expression for multi-factorial experiment using edgeR
edger differential gene expression multiple factor design
updated 6.6 years ago by ★ 28k • written 6.6 years ago by • 0
4
votes
4
replies
2.7k
views
design and contrast matrix for RNA seq analysis with three different controls
bioconductor edgeR design and contrast matrix rnaseq differential gene expression
updated 7.7 years ago by ★ 28k • written 7.7 years ago by • 0
4
votes
4
replies
2.6k
views
Non-specific filtering methodogies for ExpressionSet in R/Bioconductor
genefilter R bioconductor differential gene expression
updated 9.3 years ago by 50k • written 9.3 years ago by ▴ 830
4
votes
2
replies
1.3k
views
limma; Only fit list of certain genes/ filter eSet
limma filter genelist differential gene expression
updated 7.6 years ago by 50k • written 7.6 years ago by • 0
4
votes
1
reply
1.8k
views
NAs in continuous coefficient and fold change in `zlm`
scrnaseq MAST differential gene expression
6.7 years ago Andrew_McDavid ▴ 270
4
votes
7
replies
2.8k
views
Can we use glmQLFit instead of glmFit and then glmLRT in edgeR
edger differential gene expression glmlrt()
7.4 years ago simarsidhu25 • 0
4
votes
5
replies
1.3k
views
Differential gene expression: common changes in response to treatment across cell types
deseq2 differential gene expression
updated 6.6 years ago by ▴ 680 • written 6.6 years ago by ▴ 10
4
votes
1
reply
1.4k
views
tests for equivalence with LIMMA
limma differential gene expression equivalence TOST DOSTT
updated 9.2 years ago by 65k • written 9.2 years ago by ▴ 340
50 results • Page 1 of 1
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Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
That ll be helpful. Thank you.
Comment: Log-cpm values from limma by Shaimaa Gamal • 0
I have performed RUVg correction and extracted W, factors of unwanted variation. According to limma guide, > In the limma approach to RNA…
Comment: DSS CpG coverage threshold by j.gilbert • 0
Might be a bit late for the original poster :') but in case anyone else is wondering, the DSS user guide says: *Q: Do I need to filter out…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
Segmentation is of the whole genome, I'll write some code for doing this later today.
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
I'll take a look later. For next time, I've edited your post by enclosing the code in triple backticks (on their own link). This properly …
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A: Volcanoplot with limma - RAW P-values or Adj.P-Values
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
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