[BioC] limma and spottypes

[Gordon Smyth]

Simon,

As Ken says, spotStatus() has been replaced by controlStatus(). Be careful 
also with the syntax: two arguments are required.

You can upgrade limma from http://bioinf.wehi.edu.au/limma to get the 
corrected User Guide. (Don't upgrade from the BioC development area because 
development limma now depends on R 1.9.0dev.)

Cheers
Gordon

At 02:18 PM 22/12/2003, Ken Simpson wrote:
>Hi Simon,
>
>Looks like that part of the user guide is out of date.  controlStatus()
>should do what you want.  (do help.start(), then click on Packages and
>then limma, and consult section 3: ReadingData)
>
>Cheers,
>
>Ken
>
>On Sun, 21 Dec 2003, Simon Melov wrote:
>
> > Hi,
> > I'm trying to plot some spottypes described in the usersguide of limma
> > (section 4.6). Unfortunately, I dont seem to be able to do this if I
> > follow the instructions in the guide.
> >
> > Here is the input and output
> >
> >  > spottypes<-readSpotTypes()
> >  > spottypes
> >           SpotType                     ID Name  Color
> > 1            gene                      *    *  Black
> > 2   Calibration-1  Spot Report Product 1    *    red
> > 3   Calibration-2 Spot Report Product 10    *    red
> > 4   Calibration-3  Spot Report Product 2    *    red
> > 5   Calibration-4  Spot Report Product 3    *    red
> > 6   Calibration-5  Spot Report Product 4    *    red
> > 7   Calibration-6  Spot Report Product 5    *    red
> > 8   Calibration-7  Spot Report Product 6    *    red
> > 9   Calibration-8  Spot Report Product 7    *    red
> > 10  Calibration-9  Spot Report Product 8    *    red
> > 11 Calibration-10  Spot Report Product 9    *    red
> > 12          Empty                  Empty    * yellow
> > 13         Buffer    3XSSC  1.5M Betaine    *   blue
> > 14        No data                No data    *   pink
> > 15      Human Cot            Human Cot 1    *  green
> > 16      Mouse Cot            Mouse Cot 1    *  green
> > 17        B Actin         B-Human Actin     * purple
> > 18         Poly A                 Poly A    * orange
> > 19   Salmon Sperm           Salmon Sperm    * orange
> >  > RG$genes$Status<-spotStatus(spottypes)
> > Error: couldn't find function "spotStatus"
> >  >
> >
> > In addition, I dont seem to be able to find any mention of a
> > "spotStatus" function via search.
> >
> > Any help would be appreciated.
> >
> > thanks
> >
> > Simon.
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor