Bioconductor Memory problem

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693

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memory problem champ.load

6.0 years ago petra.lenzini • 0

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1.1k

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deseq2 memory problem

updated 6.1 years ago by Michael Love 42k • written 6.1 years ago by rbronste ▴ 60

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1.1k

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big data methylmix memory problem

updated 6.2 years ago by Martin Morgan 25k • written 6.2 years ago by perdedorium • 0

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975

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edgeR processamplicons memory problem

6.4 years ago sdalin • 0

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1.9k

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memory problem gaia

updated 7.0 years ago by Sandro Morganella ▴ 40 • written 7.0 years ago by drusmanbashir • 0

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1.7k

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oligo hta2.0 affymetrix microarrays memory problem

updated 7.6 years ago by James W. MacDonald 67k • written 7.6 years ago by svlachavas ▴ 830

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Comment: Identical samples after deseq2 batch effect removal by Michael Love 42k

I'm adding my comment to the threaded section ... I don't have any suggestions here but whatever method you're using is not appropriate up…

Comment: ANOVA like approach of edgeR by Yunshun Chen ▴ 870

If you do it this way, the dispersion estimates would be much higher than they should (as the cell type difference is not accounted for in …

Comment: ANOVA like approach of edgeR by SamGG ▴ 350

Simply remove the cell type from the model. design <- model.matrix(~targets$Status)

Answer: ANOVA like approach of edgeR by Yunshun Chen ▴ 870

You could try the followings: > design <- model.matrix(~ 0 + group) > contrast <- makeContrasts(PvsL = 0.5*(L.pregnant + B.pregnan…

Answer: Identical samples after deseq2 batch effect removal by maripane • 0

Thanks Michael, so is there a way to work around this issue? Can I somehow make sure I can remove this batch effects without overcorrecti…

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A: ANOVA-like test with edgeR

Answer: CleanUpRNAseq with a GTF that is missing mitochondria annotation data

A: TopGO: How to retrieve the gene list related to a GO ID ?

A: Error in DESeqDataSet : some values in assay are not integers

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