Downloads and more on R available at their site.
All kinds of information and tutorials are available at the Bioconductor site.
Slides (ppt)
from Katie’s
Katie’s Bioconductor workshop
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.
Email Lily Shiue with suggestions for additions to this page.