How To Handle Broad Cmap Raw Data(.Cel)

Question

[zerohsy]

Hello,I am doing the data processing of the broad cmap. However,I do not know how to handle the raw data(.cel).When I open the matarial when I download from the http://www.broadinstitute.org/cmap/cel_file_chunks.jsp,the content of the data is just be digital gibberish using the excel.I want to know how to process these data.

Answer 1

[Ashwin]

Hi,

I haven’t used CMAP data, however it seems that CMAP is a collection of expression profiles upon treatment with different drugs.

Now if you say that the raw files are .cel files, this must be Affy data and you cannot open such files in Excel.

Try the Affy package from Bioconductor. An introduction to this package is here http://www.bioconductor.org/packages/2.13/bioc/vignettes/affy/inst/doc/affy.pdf

Basically you have to use the ReadAffy() function to read the .cel files. Be sure to include the destination of the file or work in the same directory.

If you are not a "R person" use tools like chipster for easy graphical user interface http://chipster.csc.fi/

However there will be many things for you to consider like data preprocessing and quality control, than just reading in the .cel file.

Regards

Ashwin