Bioconductor Avereps

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2

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2

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496

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avereps probes average limma Microarray

updated 9 months ago by Gordon Smyth 49k • written 9 months ago by mohammedtoufiq91 ▴ 10

5

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6

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1.3k

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RSEM avereps voom limma RNASeq

16 months ago Yang Shi ▴ 10

1

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12

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2.0k

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limma avereps probe mapping microarray Agilent

updated 4.9 years ago by Gordon Smyth 49k • written 4.9 years ago by wd ▴ 30

4

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4

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3.2k

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limma duplicatecorrelation avereps

updated 7.2 years ago by Gordon Smyth 49k • written 7.2 years ago by Guido Hooiveld ★ 3.8k

4 results • Page 1 of 1

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Comment: Agilent Microarray Gene Oncology analysis gone wrong by SamGG ▴ 320

Gordon said to let coef to its default value: topTable(fit, n=20)

Comment: Can the limma package be applied to Log2 RUV-normalized data? by Shaimaa Gamal • 0

Hi Gordon, On what basis we can determine whether the dataset is large or not? I am working on a dataset of 515 samples and 5440 genes. I w…

Comment: Agilent Microarray Gene Oncology analysis gone wrong by samagbeyimodupe • 0

Thank you for the quick response. i ran the codes again and removed all the other arguments for eBayes except for fit. I ran the line of co…

Comment: Correct the batch effect in methylation analysis in R by Gordon Smyth 49k

> Is it okay to apply removeBatchEffect before a limma analysis(limma linear model)? No, you should not apply any batch correction before …

Comment: Correct the batch effect in methylation analysis in R by kyj2226 • 0

Thank you for your response Gordon :) I've already run the code below, just add batch to the limma linear model design <- model.matri…

Votes

Answer: Correct the batch effect in methylation analysis in R

Answer: enrichGOgradient color change

Answer: Filter genes by expression for voomLmFit

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