Bioconductor QualityControl

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QualityControl methylationArrayAnalysis

16 months ago zusman • 0

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644

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QualityControl Alignment QuasR

updated 2.3 years ago by Michael Stadler ▴ 350 • written 2.3 years ago by h.kozlowski • 0

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407

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folder quality QualityControl AffyExpress

2.5 years ago bastien_chassagnol • 0

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1.1k

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qc qualitycontrol arrayqualitymetrics mouse gene st 2.0 affymetrix

updated 5.8 years ago by James W. MacDonald 63k • written 5.8 years ago by n.lu • 0

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731

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qualitycontrol

updated 6.2 years ago by Mike Smith ★ 6.0k • written 6.2 years ago by XIA.PAN ▴ 20

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806

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shinymethyl minfi epic microarray methylationepic qualitycontrol

6.3 years ago chelsey.ju • 0

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898

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limma one colour agilent microarrays qualitycontrol arrayqualitymetrics

6.6 years ago Bouzid.a ▴ 20

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GWASTools qualitycontrol HumanOmni5-4BeadChip GenomeStudio illumina

updated 7.1 years ago by Stephanie M. Gogarten ▴ 840 • written 7.1 years ago by Lna • 0

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1.2k

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NUSE qualitycontrol microarray

updated 7.4 years ago by Diego Diez ▴ 760 • written 7.4 years ago by jacorvar ▴ 40

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2.0k

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rna-seq GC-Content qualitycontrol

updated 7.6 years ago by Matthew McCormack ▴ 180 • written 7.6 years ago by NS ▴ 60

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1.5k

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limma affy probe qualitycontrol design and contrast matrix

updated 8.4 years ago by Gordon Smyth 47k • written 8.4 years ago by alakatos ▴ 120

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948

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Microarray OneChannel TwoChannel DifferentialExpression Preprocessing QualityControl affy

16.1 years ago Amin Moghaddasi ▴ 130

12 results • Page 1 of 1

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Answer: DESeq2 + analysis question for design with uneven time point design by Michael Love 40k

I'd recommend reaching out to a local statistician or someone familiar with linear models in R. Unfortunately, I have to reserve my time on…

Answer: Genes with highest differential expression have very low read counts for most ge by Michael Love 40k

Have you use `lfcShrink`? Or `results` with `lfcThreshold`? Either of these are recommended for prioritizing DE genes.

Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat by Gordon Smyth 47k

Yes, it is obvious that you can use expression measurements as covariates when predicting subject phenotypes. We all do that on occasion. …

Comment: Extract Limma Adjusted Values for Plotting by ATpoint ★ 2.9k

Yes, with normalized counts on log2 scale.

Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat by Anna ▴ 20

A no I never referred to transcriptomic data when I was talking about "standard procedure" I was referring to the way we analyze longitudin…

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A: Ranges from a fasta file

Answer: NA transcript values in my Txdb

Comment: Interpret plot from DiffBind

Answer: Use with_go along with other filters in getBM function

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Scholar to Mike Smith ★ 6.0k