[BioC] limma and spottypes

Ken Simpson ksimpson at wehi.edu.au
Mon Dec 22 04:18:44 MET 2003


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Looks like that part of the user guide is out of date.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



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