[BioC] Problem with PAM using R 1.9.0

[Michelle Kittleson]

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.





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BEGIN:VCARD
VERSION:2.1
X-GWTYPE:USER
FN:Kittleson, Michelle
TEL;WORK:(410) 955-5000
ORG:;Cardiology
EMAIL;WORK;PREF;NGW:mkittle1 at 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 at jhmi.edu
N:Kittleson;Michelle
END:VCARD