Showing : differential expression • reset
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Monocle-strange differential expression results
monocle differential expression
9.8 years ago sunil.mangalam • 0
2
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2
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3.0k
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order of covariates for GLM with edgeR
edger differential expression covariate batch effect glm
updated 9.9 years ago by 53k • written 9.9 years ago by ▴ 90
3
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5
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2.6k
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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 9.9 years ago by ★ 7.9k • written 9.9 years ago by ▴ 70
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6
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4.5k
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Problem when constructing a TxDb with makeTxDbFromGFF:Error in dbGetQuery(conn,SQL) :
R differential expression rnaseqgene
10.1 years ago JunLVI ▴ 40
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4
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3.2k
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How to find significantly stably expressed miRNA with DESeq2 DE results
deseq2 microrna differential expression stable expression
10.1 years ago mariakarand ▴ 20
3
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3
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1.8k
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edgeR contrast formulation question
edger rnaseq differential expression
updated 10.1 years ago by ★ 7.9k • written 10.1 years ago by • 0
2
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2.2k
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Drastic DE result discrepancies between versions of DESeq2
deseq2 differential expression microbiome
updated 10.2 years ago by 43k • written 10.2 years ago by • 0
4
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4
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3.9k
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DESeq2: Abnormally skewed distribution of p-values
deseq2 p-value distribution differential expression
10.3 years ago • updated 10.2 years ago GFM ▴ 20
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1.1k
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Differential Expression Analyses of Entire Connectivity Map (microarray) dataset
differential expression microarray R
10.3 years ago Bioinformatist Newbie • 0
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1.2k
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Matching New Samples to Differential Expression Profile
differential expression ebseq rnaseq
10.3 years ago jbarker2 • 0
2
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4
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11k
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Limma LmFit() giving error: Error in lm.fit(design, t(M)) : incompatible dimension
limma differential expression design matrix error eset
updated 10.3 years ago by ★ 29k • written 10.3 years ago by ▴ 20
17
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4
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33k
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RPKM, CPM and TMM
edger rnaseq differential expression
updated 10.4 years ago by ★ 29k • written 10.4 years ago by ▴ 160
6
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6
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2.5k
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Can i set a path for readCodlinkSet()
r differential expression codelink
updated 10.4 years ago by ▴ 760 • written 10.4 years ago by ▴ 260
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8
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2.4k
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EdgeR: batches and samples over-specify system, how to contrast un-modeled variables?
edger glmlrt() differential expression design and contrast matrix
updated 10.4 years ago by 53k • written 10.4 years ago by • 0
2
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5
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2.3k
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Codelink differential expression and annotation
r codelink differential expression hwgcod
updated 10.4 years ago by ▴ 760 • written 10.4 years ago by ▴ 260
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2
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2.0k
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Passing contrasts as a vector gives an error
r limma differential expression
updated 10.4 years ago by 53k • written 10.4 years ago by ▴ 260
12
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10
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8.0k
views
edgeR glmLRT with test="F"?
edger dge differential expression
updated 10.4 years ago by ★ 29k • written 10.4 years ago by ★ 7.9k
1
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4
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1.5k
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How to return probelist,FC and p-value column by putting a p-value threshold in Limma
r limma differential expression
updated 10.4 years ago by 53k • written 10.4 years ago by ▴ 260
4
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4
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1.8k
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Differential expression on codelink data
r codelink differential expression
updated 10.5 years ago by ▴ 760 • written 10.5 years ago by ▴ 260
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1
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961
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Find differentially expressed values
differential gene expression differential expression edgeR
updated 10.5 years ago by 53k • written 10.5 years ago by • 0
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3
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1.7k
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Differential Expression of c.diff. microarray
arrayexpress differential expression
10.5 years ago SSK ▴ 10
1
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4
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1.6k
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Specifically expressed genes
DESeq2 specific expression rnaseq clustering differential expression
updated 10.5 years ago by 43k • written 10.5 years ago by • 0
6
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4
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3.2k
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discrepance in DESeq2 results with different design structures
deseq2 differential expression independent filtering pre-filtering design matrix
10.5 years ago Assa Yeroslaviz ★ 1.5k
0
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1
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1.7k
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ArrayExpress (finding differential expression using bioconductor+C)
arrayexpress differential expression
10.5 years ago SSK ▴ 10
0
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2
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1.7k
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EBSeq package gives NaN Values for EBMultiTest
differential expression ebseq rnaseq
10.6 years ago jbarker2 • 0
0
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1
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2.0k
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DESeq2 -- Bootstrap subsampling to estimate distribution of expression
deseq2 bootstrap differential expression
updated 10.6 years ago by 43k • written 10.6 years ago by ▴ 30
1
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2
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2.4k
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Deconvolution RNA-Seq data
rna-seq differential expression
updated 10.7 years ago by 68k • written 10.7 years ago by ▴ 10
1
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1
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2.9k
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EdgeR:Calculating differential expression within/between groups in nested designs
edger nested design matrix differential expression
updated 10.7 years ago by ★ 29k • written 10.7 years ago by • 0
5
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2
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7.8k
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Ballgown vs (voom,edgeR,DESeq,limma)
limma rnaseq differential expression voom
updated 10.8 years ago by ▴ 210 • written 10.8 years ago by ▴ 50
4
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4
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3.1k
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Two-class unpaired test using LIMMA
Limma SAM differential expression
updated 11.0 years ago by 68k • written 11.0 years ago by ▴ 310
3
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2
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7.0k
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Trying to understand differential gene expression through Venn Diagrams from the 'limma' R package: why is there a number outside my diagram?
limma r venn diagram differential expression
updated 11.0 years ago by 68k • written 11.0 years ago by • 0
131 results • Page 3 of 3
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Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
Hi, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to filtering ap…
Answer: gene Set with high AUC score but no cells assigned to cell type by Kevin Blighe ★ 4.0k
Hi, You have correctly identified the issue: AUCell's automatic threshold selection is conservative by design, aiming for specificity to…
Answer: featureCounts -L: high unassigned:mapq fraction by Kevin Blighe ★ 4.0k
Hi Katarzyna, The discrepancy arises because your samtools stats were restricted to genic regions only, where alignments are typically o…
Answer: Streamlining the computing time for MiloDE p-value correction in large dataset? by Kevin Blighe ★ 4.0k
Hi Joseph, I agree with ATpoint's suggestion that pseudobulk aggregation (e.g., via aggregateData in scran or similar) would likely be far…
Votes
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Suppress warning in RHDF5 write
Answer: Suppress warning in RHDF5 write
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