Bioconductor PhenoData

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HTqPCR phenoData esetVis pData

4.2 years ago Marcelo Laia ▴ 450

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affycoretools ReadAffy Biobase phenoData affy

updated 5.1 years ago by James W. MacDonald 68k • written 5.1 years ago by bastien_chassagnol • 0

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HtqPCR grouping visualization R phenoData

6.4 years ago mohammedtoufiq91 ▴ 10

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FCS flow cytometry bioconductor phenoData Loading Data

updated 9.0 years ago by SamGG ▴ 360 • written 9.0 years ago by smajor • 0

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Comment: Combining two proteomics datasets with limpa by Andrew Pattison • 0

Thanks heaps Gordon. I went with option 1 and no normalisation and all seems to have worked well. Cheers, Andrew

Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k

Flagging protein groups as likely contaminants in this way will be fine for a limpa analysis. The `Cont_` proteins can optionally stay in f…

Answer: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k

I think that some historical context will help here. Aaron Lun was a PhD student in my Lab back in 2015, and the analysis approach that he …

Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k

You just need the mouse identifier (controls baseline) and the group specific allelic effect.

Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Julia Broadbent • 0

Hi Emily, Just sharing a resource for handling contaminants - we use the methods described in [Frankenfield et al. (2022)](https://pubs.acs…

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A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen

Comment: limpa analysis advice

Answer: When to use edgeR or limma

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