Bioconductor QualityControl

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QualityControl methylationArrayAnalysis

4.0 years ago zusman • 0

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QualityControl Alignment QuasR

updated 5.0 years ago by Michael Stadler ▴ 350 • written 5.0 years ago by h.kozlowski • 0

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958

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folder quality QualityControl AffyExpress

5.1 years ago bastien_chassagnol • 0

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qc qualitycontrol arrayqualitymetrics mouse gene st 2.0 affymetrix

updated 8.4 years ago by James W. MacDonald 68k • written 8.4 years ago by n.lu • 0

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qualitycontrol

updated 8.9 years ago by Mike Smith ★ 6.6k • written 8.9 years ago by XIA.PAN ▴ 20

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shinymethyl minfi epic microarray methylationepic qualitycontrol

8.9 years ago chelsey.ju • 0

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limma one colour agilent microarrays qualitycontrol arrayqualitymetrics

9.2 years ago Bouzid.a ▴ 20

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GWASTools qualitycontrol HumanOmni5-4BeadChip GenomeStudio illumina

updated 9.7 years ago by Stephanie M. Gogarten ▴ 890 • written 9.7 years ago by Lna • 0

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NUSE qualitycontrol microarray

updated 10.0 years ago by Diego Diez ▴ 760 • written 10.0 years ago by jacorvar ▴ 40

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rna-seq GC-Content qualitycontrol

updated 10.2 years ago by Matthew McCormack ▴ 180 • written 10.2 years ago by NS ▴ 60

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limma affy probe qualitycontrol design and contrast matrix

updated 11.1 years ago by Gordon Smyth 53k • written 11.1 years ago by alakatos ▴ 130

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Microarray OneChannel TwoChannel DifferentialExpression Preprocessing QualityControl affy

18.7 years ago Amin Moghaddasi ▴ 130

12 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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