[BioC] limma and spottypes

[Ken Simpson]

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Looks like that part of the user guide is out of date.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.