[BioC] siggenes error message about sam.plot2

He, Yiwen (NIH/CIT) [C] heyiwen at mail.nih.gov
Tue Mar 21 17:59:11 CET 2006

Hi Mr. Schwender,

Thank you for the quick response and sorry to make the mistake to email to your personal account. I'm wondering, which email list is more appropriate for siggenes questions: SAM or BioC?

Yes, my samRestuls at d does have 31 NAs out of 21987 values. Are those NAs caused by not having enough replicates in a group? Is it true that those genes will not be selected for any delta values since the difference between expected and observed will be NA and will not meet the delta threshold? How often does NAs occur in the d values? I have used siggenes to analyze lots of datasets and this is the first time I got the sam.plot2 error.

I appreciate you help!

-----Original Message-----
From: Holger Schwender [mailto:holger.schw at gmx.de] 
Sent: Tuesday, March 21, 2006 11:33 AM
To: He, Yiwen (NIH/CIT) [C]
Cc: sam-software at yahoogroups.com; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] siggenes error message about sam.plot2

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

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.


> --- 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
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor

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