Bioconductor QualityControl

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QualityControl methylationArrayAnalysis

2.2 years ago zusman • 0

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1.0k

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QualityControl Alignment QuasR

updated 3.2 years ago by Michael Stadler ▴ 350 • written 3.2 years ago by h.kozlowski • 0

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605

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folder quality QualityControl AffyExpress

3.4 years ago bastien_chassagnol • 0

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1.4k

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qc qualitycontrol arrayqualitymetrics mouse gene st 2.0 affymetrix

updated 6.7 years ago by James W. MacDonald 65k • written 6.7 years ago by n.lu • 0

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903

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qualitycontrol

updated 7.1 years ago by Mike Smith ★ 6.5k • written 7.1 years ago by XIA.PAN ▴ 20

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998

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shinymethyl minfi epic microarray methylationepic qualitycontrol

7.2 years ago chelsey.ju • 0

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1.1k

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limma one colour agilent microarrays qualitycontrol arrayqualitymetrics

7.5 years ago Bouzid.a ▴ 20

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GWASTools qualitycontrol HumanOmni5-4BeadChip GenomeStudio illumina

updated 8.0 years ago by Stephanie M. Gogarten ▴ 870 • written 8.0 years ago by Lna • 0

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1.5k

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NUSE qualitycontrol microarray

updated 8.3 years ago by Diego Diez ▴ 760 • written 8.3 years ago by jacorvar ▴ 40

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2.4k

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rna-seq GC-Content qualitycontrol

updated 8.5 years ago by Matthew McCormack ▴ 180 • written 8.5 years ago by NS ▴ 60

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1.7k

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limma affy probe qualitycontrol design and contrast matrix

updated 9.3 years ago by Gordon Smyth 50k • written 9.3 years ago by alakatos ▴ 130

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1.2k

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Microarray OneChannel TwoChannel DifferentialExpression Preprocessing QualityControl affy

16.9 years ago Amin Moghaddasi ▴ 130

12 results • Page 1 of 1

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Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k

> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …

Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10

With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.

Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k

You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.

Answer: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k

Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…

Comment: get BM error by James W. MacDonald 65k

I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…

Votes

C: when to apply quantile normalization with voom in limma/voom framework with RNA-

A: How to know if I should use voomWithQualityWeights() or not?

A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom

Answer: Log-cpm values from limma

Awards • All

Teacher to Gordon Smyth 50k