Showing : ExpressionData • reset
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R: Confused about Limma R package output being LogFC or Log2FC
limma R ExpressionData
updated 15 months ago by 50k • written 15 months ago by • 0
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2
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1.7k
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PCA and heatmaps: most variable genes selection
DESeq2 ExpressionData heatmaps pca
2.9 years ago Clara • 0
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1.3k
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How to display or output expression data with non-unique feature labels?
Annotation ExpressionData Annotation ExpressionData
16.9 years ago Martin Morgan 25k
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1.2k
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Why is `scale-free topology` estimated as -sign(slope) * (R^2) in WGCNA?
Network StatisticalMethod WGCNA ExpressionData
3.3 years ago jol.espinoz ▴ 40
3
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2
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1.2k
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NChannelSet --> eSet/expressionSet ? How to transform?
ExpressionData ArrayExpress
updated 3.1 years ago by 50k • written 3.1 years ago by • 0
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1.1k
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How to display or output expression data with non-unique feature labels?
ExpressionData ExpressionData
16.9 years ago Kocherginsky, Masha [BSD] - HSD ▴ 10
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3
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970
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DESeq analysis with Biological replicate.
DESeq2 ExpressionData GeneExpression
updated 3.3 years ago by 42k • written 3.3 years ago by • 0
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3
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897
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Error in loading data set
ExpressionData
updated 2.3 years ago by ▴ 780 • written 2.3 years ago by • 0
1
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826
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nested design with random factor and limma???
ExpressionData limma ExpressionData limma
15.8 years ago Bettina Kulle Andreassen ▴ 20
2
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824
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Could use some advice on analyzing ranks of expressed genes in two conditions,
GeneExpression DESeq2 ExpressionData
updated 2.1 years ago by • 0 • written 2.2 years ago by ▴ 10
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821
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nested design with random factor and limma???
ExpressionData limma ExpressionData limma
15.8 years ago Gordon Smyth 50k
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3
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799
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expression data
ExpressionData ExpressionNormalizationWorkflow
updated 19 months ago by 65k • written 19 months ago by • 0
0
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1
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711
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Function createExpressionSet: Creating an ExpressionSet - Which package needed?
ExpressionData
updated 3.4 years ago by 42k • written 3.4 years ago by ▴ 40
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1
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643
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HSMMSingleCell metadata
ExperimentHubData ExpressionData CellDataSet RNASeqData
2.1 years ago karl.stamm ▴ 10
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2
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582
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Doubt about expression data as well as assay
GEOquery ExpressionData assay SummarizedExperiment ExpressionAtlas
updated 13 months ago by • 0 • written 13 months ago by • 0
3
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544
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please resolve the issue
gene ExpressionData
updated 14 months ago by 65k • written 14 months ago by • 0
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542
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edgeR testing interactions between two factors while controlling for blocking factor
edgeR ExpressionData RNASeqData
2.1 years ago Mafalda • 0
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0
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533
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Gene expression changes in one condition
RNASeq Gene ExpressionData
2.5 years ago AZ ▴ 30
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1
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360
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Time change in expression vs time change in phenotype
Transcriptomics ExpressionData DESeq2
updated 12 months ago by 42k • written 12 months ago by • 0
19 results • Page 1 of 1
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Comment: Cannot connect to ExperimentHub server by Jiayu • 0
Many thanks and it also resolved the same issue for me!
Comment: Help with running egsea() by Chris • 0
I tried egsea.ma and got this error: gsa = egsea.ma(numeric_matrix, vector_group, probe_annotation, contrasts = contrast_matrix, gs.an…
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by angelathuynh5 • 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Method to find pathways different between 2 groups by Gordon Smyth 50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by James W. MacDonald 65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Votes
Answer: Cannot connect to ExperimentHub server
Answer: confused with tximport counts abundance using salmon input
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
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