https://github.com/poisonalien/beadanalyze

Automated differential expression analysis for Illumina beadarrays (HT12 V4 arrays).
https://github.com/poisonalien/beadanalyze

differential-expression idat illumina-beadarrays microarry

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Automated differential expression analysis for Illumina beadarrays (HT12 V4 arrays).

• Host: GitHub
• URL: https://github.com/poisonalien/beadanalyze
• Owner: PoisonAlien
• Created: 2016-08-09T03:46:00.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2016-08-09T04:11:46.000Z (over 8 years ago)
• Last Synced: 2024-10-10T20:24:00.800Z (2 months ago)
• Topics: differential-expression, idat, illumina-beadarrays, microarry
• Language: R
• Size: 220 KB
• Stars: 8
• Watchers: 3
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# beadAnalyze

Automated differential expression analysis for Illumina beadarrays (HT12 V4 arrays).

This R script performs automated differential analysis from Illumina's expression  [idat](https://www.bioconductor.org/packages/devel/bioc/vignettes/illuminaio/inst/doc/EncryptedFormat.pdf) files. By default this script assumes idat files are from HT12 V4 arrays, but with little modification it should work with any arrays.

Make sure you have the following dependencies installed:

[beadarray](https://www.bioconductor.org/packages/release/bioc/html/beadarray.html), [illuminaHumanv4.db](http://bioconductor.org/packages/release/data/annotation/html/illuminaHumanv4.db.html), [limma](https://bioconductor.org/packages/release/bioc/html/limma.html), ggplot2, ggrepel

###Usage:

Clone this repo and source `analyzeBead.R`

Arguments:

`idats` = input IDAT files

`names` = Sample names for each idat file

`condition` = Sample conditions for each idat file

`ref.condition` = reference condition. 

`fdr` = FDR cutoff. Default 0.05

`pltPCA` = If TRUE performs PCA

```{r}

#Example usage with four idat files (2 control and 2 treated).

source("AnalyzeBead.R")

bead.results = beadAnalyze(idats = c("file1.idat","file2.idat","file3.idat","file4.idat"), 

  names = c("control1","control2","treated1","treated2"), 

  condition = c("control","control","treated","treated"), 

  ref.condition = "treated",

  fdr = 0.05, plotPCA = T) 

```