[BioC] siggenes error message about sam.plot2

[He, Yiwen (NIH/CIT) [C]]

Hi, I tried to reach the maintainer of the siggenes package without much
success, so I'm forwarding my question to both lists hoping that some
one may have experienced the same problem and know how to fix it. Your
help will be highly appreciated!
Yiwen

-----Original Message-----
From: He, Yiwen (NIH/CIT) [C] 
Sent: Thursday, March 16, 2006 4:59 PM
To: 'holger schwender'
Subject: siggenes error message about sam.plot2

Hello Mr. Holger,

I have been able to use your siggenes package successfully but recently
got an error about pos.stats when I tried to make a sam plot for a
particular dataset.

dd is a matrix of 21987 x 44, 5 groups:
> table(cl)
cl
 1  2  3  4  5
 7 10 10 11  6

> samResults<-sam(dd,cl, B=B, rand=rand.sd)
> plot(samResults, 1.6)
Error in sam.plot2(x, delta = y, pos.stats = pos.stats, sig.col =
sig.col,  :        pos.stats must be either 0 (statistics are not
displayed),
1 (stats are displayed in the upper left of the plot), or 2 (lower
right).

I got the same message when I call directly:

> sam.plot2(samResults, 1.6)
Error in sam.plot2(samResults, 1.6) : pos.stats must be either 0
(statistics are not displayed), 1 (stats are displayed in the upper left
of the plot), or 2 (lower right).

I was able to make it work by explicitly specify:

> plot(samResults, 1.6, pos.stats=2) OR
> sam.plot2(samResults, 1.6, pos.stats=2)

But I don't understand why the internal parameter is not working. 

I also tried to subset the data and interestingly plotting was fine for
the first two groups (21987 x 17), but not for the first four groups
(21987 x 38). But when trying some other datasets with > 2 groups, it
worked fine.

I hope to get some insight from you. I tried both R 2.1/siggenes 1.2.17
and R 2.2/siggenes 1.4.


Also, just to confirm with you, when using R 2.1 and siggenes 1.2.17 for
another dataset, I got an error:

> samResults<-sam(dd,cl, B=B, rand=rand.sd)
Error in cut.default(s, quan, include.lowest = TRUE, right = FALSE) :
        'breaks' are not unique

But when I tried R 2.2 and siggenes 1.4 on the same data, it worked
fine. Should I be concerned about my data or was it some bug in siggenes
that is fixed in 1.4?

Thank you very much for your help, and I look forward to your answer.

Yiwen He
mAdb Team
BIMAS/DCB/CIT/NIH