Bioconductor No replicates

Showing : no replicates • reset

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1.1k

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methylsig no replicates dmr

7.5 years ago nilaycan • 0

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deseq2 without replicate no replicates

updated 7.7 years ago by Michael Love 43k • written 7.7 years ago by Tony • 0

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12k

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deseq2 no replicates high p-adj values

updated 3.5 years ago by Michael Love 43k • written 8.3 years ago by Mahtetie • 0

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2.9k

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rnaseq edger DGE no replicates

8.5 years ago • updated 8.4 years ago Stefany Solano • 0

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1.7k

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diffhic estimate dispersion value glm no replicates deseq

updated 8.8 years ago by Aaron Lun ★ 29k • written 8.8 years ago by hwick1 ▴ 20

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5.8k

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ATAC differential binding analysis no replicates DEseq2 chromatin

8.9 years ago • updated 8.8 years ago BioinfGuru ▴ 70

6 results • Page 1 of 1

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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

Aaron Lun was a PhD student in my Lab back in 2015, when he posted the answers about allele-specific expression that you and Mike Love have…

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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