Harshlight: a "corrective make-up" program for microarray chips

Mayte Suárez-Fariñas, Maurizio Pellegrino, Knut M. Wittkowski and Marcelo Magnasco


Harshlight is a tool for the automatic recognition of blemishes on HDONA microarrays. It is implemented as an R package add-on to the Bioconductor project. It is written in R with a C library implementing the most computationally intensive image recognition tasks.
To install the package, download Harshlight and install it like any other R add-on package. (Instructions for doing so are given in the  R FAQ on R add-on packages.)
For the Unix version, use the command "R CMD INSTALL /path/to/pkg_version.tar.gz" in the shell prompt.
For the Windows version, use the option "Install package(s) from local zip files..." from the menu "Packages".

Once installed, it is very easy to use!

>library(Harshlight)
>load('my.affybatch')
>harsh.affybatch <- Harshlight(my.affybatch,report.name='MyReport.ps')

And you can continue processing your harshlighted affybatch as with the original one ...

>harsh.mas5 <- mas5(harsh.affybatch)
>harsh.rma  <- rma(harsh.affybatch)


(If you do not have your own data, dowload our small example here)

Examples of Reports:
 
First Page  P15  P22  P22  P22  P22  P22 

We have a gallery of Harshlight Reports for more than 150 chips showing a large variety of blemishes.

If you find a bug, please contact Maurizio Pellegrino:  mpellegri@rockefeller.edu


The package is maintained by Maurizio Pellegrino (mpellegri@rockefeller.edu) and Yupu Liang (liangy@rockefeller.edu)


References:

- Harshlight: a "corrective make-up" program for microarray chips, Mayte Suarez-Farinas*, Maurizio Pellegrino*, Knut M Wittkowski and Marcelo O Magnasco, BMC Bioinformatics 2005 Dec 10; 6(1):294
- "Harshlighting" small blemishes on microarrays, Suarez-Farinas M, Haider A, Wittkowski KM., BMC Bioinformatics. 2005 Mar 22;6(1):65.

Supplementary Material:
- SIprobecomposition.pdf

Supplementary Software:
- Helpers is an R add-on package. It is written in R with a C library implementing the most computationally intensive prcedures.For the moment,it can help you to write the AffyBatch to CEL files(txt format only and you need to have the original CEL files). We may add more function to it later.

If you find a bug or have comments, please contact Yupu Liang:  liangy@rockefeller.edu

For the Unix version, use the command "R CMD INSTALL /path/to/pkg_version.tar.gz" in the shell prompt.
For the Windows version, use the option "Install package(s) from local zip files..." from the menu "Packages".

Once installed, it is very easy to use!

>library(Harshlight)
>library(Helpers)
#read in the CEL files from your working director
>org_data = ReadAffy()
>harsh_data = Harshlight(org_data,report.name='MyReport.ps')
#write the fixed AffyBatch to CEL files that use 'harsh_' as the prefix of original CEL file name
>out = WriteAbatch(harsh_data,prefix='harsh')


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Last update: January 12, 2006   by Mayte Suárez-Fariñas.