Bioconductor Microarrays

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limma sample size microarrays statistical power

7.6 years ago eleonoregravier ▴ 70

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microarrays xml RCurl libxml2 libcurl

updated 8.7 years ago by Martin Morgan 25k • written 8.7 years ago by farahqureshi5 • 0

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whole human genome microarray 4x44k microarrays

8.7 years ago farahqureshi5 • 0

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limma cmap microarrays differential gene expression

8.8 years ago kevin.m.hao ▴ 10

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limma design matrix limma limma contrast matrix microarrays

9.4 years ago • updated 9.3 years ago miyuki_iii ▴ 10

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Comment: Getting a large intercept with DESeq2 by Michael Love 43k

Thanks James -- Denise you can check the "note on factor levels" in the vignette. And I'd recommend `plotCounts()` for looking at individu…

Comment: Getting a large intercept with DESeq2 by James W. MacDonald 68k

As a trivial example, consider this: ``` > model.matrix(~Treatment, data.frame(Treatment = factor(rep(1:3, each = 4)))) (Intercept) Tre…

Answer: Getting a large intercept with DESeq2 by James W. MacDonald 68k

The default parameterization in R is a treatment-contrasts parameterization that sets one of your groups as the baseline. So the intercept …

Answer: Must I do pseudobulk analysis on Cell Surface Protein Labeling data of Single C by ATpoint ★ 5.0k

There is no "MUST", but pseudobulk aggregation is beneficial to a) enable use of tested and robust methods such as limma (though it could u…

Answer: Post translational modifications and phosphoproteomics in limpa? by Gordon Smyth 53k

Yes, we use limpa for PTMs ourselves. I assume your data is preprocessed so that each row corresponds to a PTM. You replace dpcQuant() with…

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Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif

Using edgeR or DESeq2 to analyze allele-specific expression?

Answer: DESeq2 design for haplotype MPRA

Answer: Failure to download resources (MeSHDb) from AnnotationHub

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