Bioconductor Complex-design

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limma complex-design paired design

updated 6.8 years ago by Aaron Lun ★ 28k • written 6.8 years ago by ML18 ▴ 10

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rnaseqpower sspa sample size sequencing complex-design

updated 8.9 years ago by m.van_iterson ▴ 20 • written 8.9 years ago by roser.navarro • 0

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limma paired samples complex-design

9.1 years ago • updated 9.0 years ago aec ▴ 90

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4.3k

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limma model matrix limma design matrix complex-design

updated 9.6 years ago by Aaron Lun ★ 28k • written 9.6 years ago by Guido Hooiveld ★ 4.1k

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deseq2 multiple factor design complex-design

updated 9.9 years ago by Michael Love 43k • written 9.9 years ago by sifujio • 0

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7.0k

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combat software error rnaseq complex-design

updated 10.3 years ago by Peter Langfelder ★ 3.0k • written 10.3 years ago by Stefano Mangiola ▴ 20

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2.6k

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edgeR complex-design

updated 10.3 years ago by James W. MacDonald 67k • written 10.3 years ago by lwc628 ▴ 20

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Comment: Is there a way to do DEG analysis across two batches sharing one sample only? by georgeyu703 • 0

Michael, Thank you very much!

Comment: Is there a way to do DEG analysis across two batches sharing one sample only? by Michael Love 43k

Yes, with the knowledge that, it is expected to be underpowered.

Comment: Is there a way to do DEG analysis across two batches sharing one sample only? by georgeyu703 • 0

Thank you, Michael. How? Could you provide more details? Can I just do it as usual, I mean to include batch in the model?

Answer: Is there a way to do DEG analysis across two batches sharing one sample only? by Michael Love 43k

The short answer is yes, you can use even a single sample to estimate the batch effect (and therefore control for it in otherwise confounde…

Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by alserg ▴ 280

`NES > 0` means that your gene set has more genes with positive logFC/stat. In your case these genes should be up in Subset1. However, if y…

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Answer: SingleCellExperiment convenience function for metadata+expression?

How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.

Answer: EdgeR Biological CVs

Answer: Error in download.file for TCGAutils::symbolsToRanges

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