I've asked Genelogic for the dilution data but have not received it.
What can I do?
Contact Mike Elashorff at Genelogic. However, you no longer need it to participate.
Why are the original and new assessments? The original is described in the manuscript. The new is a new set of assessments that incldude suggestions made by participants. We will soon have a manuscript describing it.
Why are there more spike-ins than described by Affymetrix? Read this blurb.
Can I get the R package with the assessment functions? Sure, the
latest release (source and win32 binary) is available from Bioconductor.
How should I normalize the dilution data? We recommend each dilution group be normalized separtely since the assumptions of overall similarity does not hold otherwise. Notice this defines six groups with 10 arrays each. However, we use control genes to try to correct for dilution as described in the manuscritp. So you can try submitting results that have been normalized all together.
What is the NO-COMP check box for? If you mark the check-box your results will not be part of the competition table.
Can I upload just one data set? Yes! As long you submit one of the data set the assessments will be performed. You can submit any combination you want.
Can I see the code that does the assessments?
Here is the R script the server runs.
Most of the work is done in the
affycomp R package, which is loaded by this script.
For the MA plot in the reports, you chose only 14 of the 59 arrays.
Which ones and why?
We chose 1521a99hpp_av06, 1521b99hpp_av06, 1521c99hpp_av06,
1521d99hpp_av06, 1521e99hpp_av06, 1521f99hpp_av06, 1521g99hpp_av06,
1521h99hpp_av06, 1521i99hpp_av06, 1521j99hpp_av06, 1521k99hpp_av06,
1521l99hpp_av06,1521m99hpp_av06, and 1521q99hpp_av06.
We chose 14 so that concentrations/probeset interactions are balanced
and to avoid having so many points that the graphs were confusing.
In our experience, different (balanced) choices provide similar plots.
Can I submit compressed files? Not yet. We are working on it.
I want to use R to compute expression measures. Are there rda files available? Download the affy package and contact us.