[BioC] siggenes error message about sam.plot2

[Holger Schwender]

Hi Yiwen,

first of all, sorry that I have not answered your email yet. The reason for
this might be that you have sent your email to my yahoo account which I do
not use anymore. Please use this email address for further request.

Now to the second problem: Yes, this bug has been fixed in version 1.3.x of
siggenes.

To the sam.plot2 problem: I actually do not really know why this happens.
But it might be a bug in sam.plot2. Please let me know if there is any
missing value in samResults at d. If so, this might cause the error and I will
fix this bug.

Best,
Holger




> --- Ursprüngliche Nachricht ---
> Von: "He, Yiwen \(NIH/CIT\) [C]" <heyiwen at mail.nih.gov>
> An: <sam-software at yahoogroups.com>, <bioconductor at stat.math.ethz.ch>
> Betreff: [BioC] siggenes error message about sam.plot2
> Datum: Tue, 21 Mar 2006 10:00:18 -0500
> 
> 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
> 
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> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> 

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