Showing : differential gene expression • reset
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featureCounts creating fragments and high NoFeatures value
featurecounts bioconductor differential gene expression star
updated 8.7 years ago by ★ 3.6k • written 8.7 years ago by ▴ 10
2
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5
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DESeq2 problem with outlier replacement in paired multi-factor design
deseq2 differential gene expression multiple factor design paired design
8.7 years ago gregory.l.stone ▴ 10
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6
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1.9k
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Confusing: identify differentially expression genes (DEG) perturbed by a drug in Limma
limma cmap microarrays differential gene expression
8.7 years ago kevin.m.hao ▴ 10
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4
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4.1k
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Simultaneously adding two different covariates in the model gives error in DESeq2.
deseq2 dexseq rnaseq differential gene expression differential exon usage
updated 8.8 years ago by 43k • written 8.8 years ago by ▴ 40
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3
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WGCNA Co-expression
microarray differential gene expression module
updated 8.8 years ago by ★ 3.0k • written 8.8 years ago by • 0
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6
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1.6k
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design of edgeR GLM test
edger differential gene expression glmlrt()
8.8 years ago simarsidhu25 • 0
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3.9k
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gff error in featureCounts
differential gene expression
8.8 years ago esu2001 • 0
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Can we use glmQLFit instead of glmFit and then glmLRT in edgeR
edger differential gene expression glmlrt()
8.8 years ago simarsidhu25 • 0
2
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2
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9.3k
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edgeR: How is FDR calculated for logFC? (False Discovery Rate)
edgeR bioconductor fdr statistics differential gene expression
8.8 years ago jol.espinoz ▴ 40
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3
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2.4k
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Error in ball gown command
rnaseq ballgown differential gene expression
updated 8.8 years ago by ▴ 650 • written 8.8 years ago by ▴ 10
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3
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1.2k
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F test for two phenotypic and multiple phenotypic categories.
limma f test differential gene expression
updated 8.9 years ago by ★ 7.9k • written 8.9 years ago by ▴ 70
2
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5
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4.5k
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processing data with 2 rep or one replicate by ballgown
ballgown differential gene expression
updated 9.0 years ago by ▴ 210 • written 9.0 years ago by • 0
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3
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3.3k
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DiffBind cut off clarification
diffbind differential gene expression
updated 9.0 years ago by ▴ 670 • written 9.0 years ago by • 0
4
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2
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1.6k
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limma; Only fit list of certain genes/ filter eSet
limma filter genelist differential gene expression
updated 9.0 years ago by 53k • written 9.0 years ago by • 0
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3
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1.4k
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the output DEGs of limma analyzing RNA-seq data is just 1/3 of those by Tophat-CuffDiff
differential gene expression voom limma RNA-seq
updated 9.0 years ago by 53k • written 9.0 years ago by • 0
0
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2
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992
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Table export from R
deseq2 differential gene expression
9.0 years ago jyoti.kapali • 0
2
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5
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1.8k
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Limma-Voom which of two models is correct?
limma-voom rnaseq differential gene expression
9.0 years ago Javier Gutierrez-Achury • 0
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2
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1.3k
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Differential expression of one group agains all samples
deseq2 mirna differential gene expression
updated 9.0 years ago by ▴ 690 • written 9.0 years ago by ▴ 10
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3
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1.8k
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Interaction term analysis using ballgown
ballgown stringtie voom limma differential gene expression rnaseq
updated 9.0 years ago by ▴ 210 • written 9.0 years ago by ▴ 10
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3
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3.6k
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Fisher exact test
rnaseq differential gene expression
updated 9.0 years ago by ▴ 980 • written 9.0 years ago by • 0
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13
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5.0k
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DESeq2: collapseReplicates error
deseq2 rnaseq differential gene expression
9.1 years ago ta_awwad ▴ 10
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4
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3.1k
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design and contrast matrix for RNA seq analysis with three different controls
bioconductor edgeR design and contrast matrix rnaseq differential gene expression
updated 9.1 years ago by ★ 29k • written 9.1 years ago by • 0
0
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0
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940
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How to get differentially expressed genes in "timecourse" package ?
timecourse differential gene expression
9.1 years ago moradzadeh_k921 • 0
3
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6
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2.5k
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Clarification MAplot and FDR in EdgeR
edgeR MAplot rnaseq differential gene expression
updated 9.1 years ago by 53k • written 9.1 years ago by • 0
6
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13
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4.2k
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DEseq2 with limited gene set
DEseq2 differential gene expression
9.1 years ago dmr210 • 0
4
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6
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3.2k
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How to carry out differential gene expression starting with a table of TMM normalised values without access to the raw reads?
edger raw reads TMM normalised values DGEList differential gene expression
updated 9.2 years ago by ★ 13k • written 9.2 years ago by ▴ 30
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4
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5.5k
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Filtering lowly expressed genes in voom-limma analysis
voom limma rna-seq differential gene expression
updated 9.2 years ago by 53k • written 9.2 years ago by ▴ 110
4
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2
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2.4k
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DESeq2: Shrinkage is inverting fold-changes
deseq2 differential gene expression
updated 9.2 years ago by 43k • written 9.2 years ago by ▴ 690
4
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6
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1.8k
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Differential expression across gene features
limma deseq2 differential gene expression
written 9.4 years ago by ▴ 90
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0
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1.2k
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[EBSEQ] Strange NA values
ebseq differential gene expression
9.3 years ago jean.keller ▴ 10
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5
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3.0k
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edgeR- DE analysis with no replicates
edger differential gene expression without replicate nested design help
updated 9.3 years ago by ★ 29k • written 9.3 years ago by • 0
2
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1
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1.2k
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edgeR - testing interaction in a scenario of 2 tissues and 2 ages
edgeR R differential gene expression differential expression
updated 9.3 years ago by ★ 29k • written 9.3 years ago by • 0
2
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2
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3.7k
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Why Pathview shows just red color (up-regulated genes) on a pathway?
Pathview pathway analysis differential gene expression
updated 9.3 years ago by ★ 1.6k • written 9.3 years ago by ▴ 20
4
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7
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2.3k
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assigning differential exons to trascripts
dexseq rsem differential exon usage differential gene expression
updated 9.3 years ago by 68k • written 9.3 years ago by ★ 1.5k
0
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7
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2.6k
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DESeq2 with interest only for 1 gene
R deseq2 differential gene expression help
9.3 years ago fischer87 • 0
0
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2
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3.5k
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Use surrogate variables on DESeq2
deseq2 sva deseq differential gene expression
updated 9.3 years ago by ▴ 20 • written 10.1 years ago by ▴ 40
3
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1
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1.5k
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how duplicates reads would affect Differential expression analysis results
limma differential gene expression bioconductor
updated 9.3 years ago by ★ 29k • written 9.3 years ago by • 0
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1
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1.1k
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challenging design matrix
limma design matrix differential gene expression limma
updated 9.3 years ago by 53k • written 9.3 years ago by • 0
2
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2
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1.6k
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EdgeR experimental design matrix
edger differential gene expression experimental design
updated 9.3 years ago by ★ 29k • written 9.3 years ago by • 0
0
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0
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1.3k
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[EBSeq] Normalization and DE genes detection
ebseq normalization differential gene expression
9.4 years ago jean.keller ▴ 10
5
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12
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6.1k
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Differential expression analysis: comparison of DESeq2 and edgeR robust results
deseq2 edgeR differential gene expression
updated 9.4 years ago by ★ 29k • written 9.4 years ago by ▴ 90
6
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12
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20k
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Problem making DESeq dataset; Error all variables in design formula must be columns in colData
deseq2 deseq counts rnaseq differential gene expression
updated 9.4 years ago by 43k • written 9.4 years ago by ▴ 10
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1
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1.7k
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How to get diff expresion results from sam files
differential gene expression sam
updated 9.4 years ago by ★ 29k • written 9.4 years ago by • 0
1
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1
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2.0k
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How to inteprate distances calculated by cmdscale?
differential gene expression cmdscale mds
9.4 years ago Adam • 0
1
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1
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1.8k
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CellCODE estimate cell proportions SPV analysis grouping comparisons faulty
CellCODE differential gene expression
9.5 years ago christopher.clarskon15 ▴ 20
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1
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1.3k
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Functions of DESeq2 package
deseq2 differential gene expression rna-seq
updated 9.5 years ago by ★ 13k • written 9.5 years ago by • 0
1
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1
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1.9k
views
Differential binding using csaw
csaw differential binding analysis chipseq differential expression differential gene expression
updated 9.5 years ago by ★ 29k • written 9.5 years ago by ▴ 10
1
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1
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1.8k
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edgeR, DE between 4 different samples
edger differential gene expression GLM Tutorial
updated 9.5 years ago by 68k • written 9.5 years ago by • 0
2
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5
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3.6k
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Programs used in RNA-seq workflow
deseq2 bioconductor workflows differential gene expression rnaseqgene
9.5 years ago cirisarri95 • 0
7
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18
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4.7k
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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 9.5 years ago by ★ 7.9k • written 9.5 years ago by • 0
272 results • Page 4 of 6
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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…
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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
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