I've been unable to successfully run PAM in Excel or R since installing the newest version of R 1.9.0. In detail, the problems have been: Since I downloaded the new version of R, PAM version 1.12 for Excel doesn't work anymore. It tells me that it's not connected to R anymore. So I uninstalled PAM 1.12 and went to the PAM website to re-install the new version, PAM 1.20, figuring maybe that would help. PROBLEM #1: But now it won't let me install PAM 1.20, saying "Please install R version 1.7.0 or higher first," even though R 1.9.0 is already installed! PROBLEM #2: Since I couldn't install PAM for Excel, I figured I'd try to use the PAM for R version. When I did, I got the error below: Error: 'codes' is defunct. See ?Defunct. I don't know what to do, though, because I never use the word "codes" anywhere in the code (see below). Has anyone experienced this, or know how to fix it? Thanks, Michelle Kittleson > library(pamr) > mmk.data <- pamr.from.excel("inirma.pambxtrain.txt", 18, sample.labels=TRUE) Read 399906 items Read in 22215 genes Read in 16 samples Read in 16 sample labels Make sure these figures are correct!! > mmk.train <- pamr.train(mmk.data) 123456789101112131415161718192021222324252627282930> > mmk.train threshold nonzero errors 1 0.000 22215 2 2 0.124 19864 2 3 0.248 17443 2 4 0.371 15077 2 5 0.495 12880 2 6 0.619 10850 2 7 0.743 9056 2 8 0.866 7432 2 9 0.990 5929 2 10 1.114 4693 2 11 1.238 3653 2 12 1.361 2825 2 13 1.485 2129 2 14 1.609 1566 2 15 1.733 1142 2 16 1.856 809 2 17 1.980 576 2 18 2.104 389 1 19 2.228 277 1 20 2.351 188 1 21 2.475 120 1 22 2.599 69 1 23 2.723 38 1 24 2.847 22 1 25 2.970 8 1 26 3.094 5 1 27 3.218 4 1 28 3.342 2 1 29 3.465 2 1 30 3.589 0 8 > mmk.results<- pamr.cv(mmk.train, mmk.data) Fold 1 :123456789101112131415161718192021222324252627282930 Fold 2 :123456789101112131415161718192021222324252627282930 Fold 3 :123456789101112131415161718192021222324252627282930 Fold 4 :123456789101112131415161718192021222324252627282930 Fold 5 :123456789101112131415161718192021222324252627282930 Fold 6 :123456789101112131415161718192021222324252627282930 Fold 7 :123456789101112131415161718192021222324252627282930 Fold 8 :123456789101112131415161718192021222324252627282930 Error: 'codes' is defunct. See ?Defunct. -------------- next part -------------- BEGIN:VCARD VERSION:2.1 X-GWTYPE:USER FN:Kittleson, Michelle TEL;WORK:(410) 955-5000 ORG:;Cardiology EMAIL;WORK;PREF;NGW:mkittle1@jhmi.edu N:Kittleson;Michelle END:VCARD BEGIN:VCARD VERSION:2.1 X-GWTYPE:USER FN:Kittleson, Michelle TEL;WORK:(410) 955-5000 ORG:;Cardiology EMAIL;WORK;PREF;NGW:mkittle1@jhmi.edu N:Kittleson;Michelle END:VCARD