Bioconductor Ncbi geo

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NCBI GEO

updated 4.2 years ago by SAn • 0 • written 9.0 years ago by maedakus ▴ 10

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geoquery ncbi geo biobase

6.2 years ago cschot3 • 0

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limma differential gene expression ncbi geo affymetrix microarrays

updated 6.2 years ago by Aaron Lun ★ 28k • written 6.2 years ago by Francesca McGrath • 0

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frma barcode geneexpression gsm ncbi geo

updated 7.2 years ago by Matthew McCall ▴ 830 • written 7.2 years ago by diana.elassal • 0

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limma microarray bioconductor ncbi geo

updated 8.0 years ago by Gordon Smyth 52k • written 8.0 years ago by kevin.m.hao ▴ 10

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geoquery ncbi geo geo data

8.2 years ago fongchunchan ▴ 30

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Answer: Selection of correct coefficients or contrasts in DESeq2 by swbarnes2 ★ 1.4k

I think you need to include the design you used, and the command you used to call it. The simplest answer is that your two ways of doing t…

Comment: Csaw normalization strategies - general inquiry by Luca • 0

Hello Aaron, About the IP efficiencies, yes definitely and for us, to complicate this experiment further, these batches were generated by …

Comment: How to compare expression levels of genes between scRNAseq and bulkRNAseq? by Quang NN ▴ 10

Thank you ATpoint for your response. In bulkRNAseq, I did have two cell types to compare. But, I want to also see if bulkRNAseq might have …

Answer: Why select top highly expressed genes based on normalized counts, but then plot by ATpoint ★ 4.6k

The choice of variable genes is typically part of a QC process. You select genes that in an unbiased fashion (unbiased because variance cal…

Comment: How to compare expression levels of genes between scRNAseq and bulkRNAseq? by ATpoint ★ 4.6k

My take is that RNA-seq (be it bulk or single-cell) is inherently relative. I don't think you can really "compare" the absolute expression …

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Answer: Csaw normalization strategies - general inquiry

A: DESeq2 interaction term

Comment: Recount3 data correspond to TCGA data

Answer: DESeq2- merging technical vs biological replicates

Answer: SingleCellExperiment convenience function for metadata+expression?

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Scholar to Aaron Lun ★ 28k