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Identification and correction of previously unreported spatial phenomena using raw Illumina BeadArray data

Mike L Smith, Mark J Dunning, Simon Tavaré and Andy G Lynch

 

Data Sets

 

To minimize the downloading of unwanted data each array section mentioned in the manuscript is available individually. Each tar.gz file contains the .tif image of the array section, along with a .bab file, which contains the both .locs and .txt file information in a compressed format.

The .bab files can be decompressed using the BeadDataPackR package, available from Bioconductor:

These file are still quite large (approx 55-75MB) and we have a limited amount of bandwidth, so please only download those arrays that you need.

 

Human-WG6 V2 Expression Array

 

 

CNV370-Duo Genotyping Array

 

 

Scripts

 

Two R scripts are also provided. These scripts are also available as additional files 1 and 2 accompanying the paper:

  • allFunctions.R provides every function that was created as part of the analysis and can be sourced into R using the source() command.
  • allScripts.R can be run to reproduce each of the images used in the paper and the additional files. It expects the datasets provided above to be in two folders called "Expression" and "CNV" respectively.

 

R Data Objects

 

We have included a subset of these arrays in two .rda files that were created immediately after the data were read into R using the beadarray package:

  • BLDataExprs.rda contains the first four sections from chip 4343238066 (A_1, A_2, B_1, B_2).
  • BLDataCNV.rda contains the three sections from the copy number chips listed above.