Thanks all the reply! haojie -----Original Message----- From: Holger Schwender [mailto:holger.schw@gmx.de] Sent: Thursday, September 16, 2004 12:39 PM To: Robert Gentleman Cc: haojie.wu@vanderbilt.edu; bioconductor@stat.math.ethz.ch Subject: Re: [BioC] about siggenes There is a problem with the vignette (some chunk does not work) when the package is built under R 2.0.0. Thus, there is also no manual in the devel version of siggenes even though I have written one (the Release 1.4 version does not contain a manual). Since everything else works and since I will write a new manual/vignette for the new rewritten version of siggenes this week-end, I have not corrected this. So you will not get the pdf using openVignette(). However, you can get the chunks in the vignette using the function vExplorer() of the tkWidget package. To the problem with the fudge factor (the error message you get): This happens if there are less than 101 genes with differing standard deviations. Since SAM is actually thought for the analysis of several hundred genes I have not corrected this "bug" up to now. This means it will be corrected in the next version. There you must have at least 25 genes with differing standard deviations (this limit was set by me, actually the computation would work for less than 10 genes) to compute Tusher's fudge factor. Otherwise, another method is used. The new version is also much, much faster. While the old version needs about 1 min to compute the fudge factor for the Plus2 chip of Affymetrix, the new one needs less than 10 seconds -- even if you specify more values for alpha. HTH, Holger > The vignette comes with the package, if it was properly installed. > You should be able to do something like: > see either vignette, > or openVignette (in Biobase) > > Robert > > On Wed, Sep 15, 2004 at 10:54:41AM -0500, haojie wrote: > > Hi, all > > > > I need to run sam function in the siggenes package, but I can't find the > > vignette of siggenes package in bioconductor website ( > > <http: www.bioconductor.org=""/> http://www.bioconductor.org/). Is there > > any detailed manual about the siggenes package? > > > > The problem I encountered is when I run sam function, for example : > > sam(mydata,cl) > > there is an error : > > Error in var(v) : missing observations in cov/cor. > > How can I find the problem? And what should I do to shape my dataset for > > sam function? > > > > Thanks for your help! > > haojie > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > -- > +--------------------------------------------------------------------- ------ + > | Robert Gentleman phone : (617) 632-5250 > | > | Associate Professor fax: (617) 632-2444 > | > | Department of Biostatistics office: M1B20 > | > | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu > | > +--------------------------------------------------------------------- ------ + > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -- NEU: GMX ProMail mit bestem Virenschutz http://www.gmx.net/de/go/mail +++ Empfehlung der Redaktion +++ Internet Professionell 10/04 +++