Bioconductor TimeSeriesExperiment

Showing : TimeSeriesExperiment • reset

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1.9k

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R GillespieColin ArrayExpress import TimeSeriesExperiment

updated 7 months ago by jacorvar ▴ 40 • written 19 months ago by eraldagjika ▴ 20

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1.7k

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LRT Design DESeq2 doseResponse TimeSeriesExperiment

updated 2.7 years ago by Michael Love 42k • written 2.7 years ago by Mari • 0

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964

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QTL fourier TimeSeriesExperiment timecoursedata

3.1 years ago Daphne • 0

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918

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Proteomics limma repeatedmeasures TimeSeriesExperiment

18 months ago proteome_AO • 0

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811

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TimeSeriesExperiment Regression top limma

updated 2.7 years ago by James W. MacDonald 65k • written 2.7 years ago by Eleni • 0

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800

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TimeSeriesExperiment RNASeq design DESeq2

updated 2.4 years ago by Michael Love 42k • written 2.4 years ago by Kesava • 0

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791

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TimeSeriesExperiment

updated 3.0 years ago by Michael Love 42k • written 3.0 years ago by curiousmind007 ▴ 10

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776

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DESeq2 single-timeseries TimeSeriesExperiment

updated 19 months ago by Michael Love 42k • written 20 months ago by Jigyasa • 0

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646

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DESeq2 MultipleFactors TimeSeriesExperiment

updated 20 months ago by Michael Love 42k • written 20 months ago by Maria • 0

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627

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DESeq2 TimeSeriesExperiment

updated 19 months ago by Michael Love 42k • written 19 months ago by Jason • 0

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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)`)?

Answer: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k

If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…

Votes

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

Answer: How to save the DEXSeq results

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Popular Question to Gyan Prakash Mishra ▴ 10