R/Bioconductor info



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All kinds of information and tutorials are available at the Bioconductor site.



Slides (ppt) from Katie’s 3/4/04 workshop on programming in R.



Katie’s  Bioconductor workshop 3/11/04:

v     Slides (ppt) for her talk.

v     Demo file for loading spotted array files.  (available at the Bioconductor site, under Documentation, Lab Materials)

v     Example details file.

v     Example import script, used with the example details file above. 


v     For your own test use, to practice what Katie demonstrated, create a test directory.  You will need:

Ř      .gpr files for all the arrays to be analyzed.

§        Modify the details file with the information for your arrays; put them in alphanumeric order by the .gpr filenames.  Place the modified details file in your test directory.

§        If desired, modify the name of the details file itself and in the importGPR function call.

§        Place only the .gpr files to be analyzed in your test directory.

Ř      a “standard” GenePix galfile (with a 21-line header) for the arrays; spot IDs in column 5 will be used for spot/gene labels.

§        Modify the importGPR function call with the name of the galfile.

§        Modify the grid specifications (number of spot, grid rows/columns) and columns specifying controls and plate info in the import script line for “grid” to reflect your array specs.

§        Place the galfile and the modified import script into your test directory.

v     Launch R, and source your import script.









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