[BioC] limma and spottypes

[Gordon Smyth]

At 05:58 PM 22/12/2003, Simon Melov wrote:
>Thanks for the speedy response. After upgrading to the latest version of 
>limma it works fine. However, I now would like to just plot some spots 
>from the spot types file. I'm sure its pretty simple, but Ive tried all 
>sorts of permutations of the controlStatus function, but cant seem to get 
>it to work. Here is an example, I would like to just plot "genes", as well 
>as "Buffer" in an MA plot for example. I already assigned colors in the 
>spottype file. What would be the appropriate functions?

Don't change the controlStatus function, just use

plotMA(RG,value=c("gene","Buffer"),col=c("black","blue"))

General rule: controlStatus sets permanent attributes, but you can 
over-ride them by specifying values, colors etc explicitly.

Another way to achieve the same thing would be to temporarily subset the RG 
object.

Gordon

>thanks
>
>Simon.
> >types<-readSpotTypes()
> > types
>          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<-controlStatus(types,RG)
>Matching patterns for: ID Name
>Found 25088 gene
>Found 32 Calibration-1
>Found 32 Calibration-2
>Found 32 Calibration-3
>Found 32 Calibration-4
>Found 32 Calibration-5
>Found 32 Calibration-6
>Found 32 Calibration-7
>Found 32 Calibration-8
>Found 32 Calibration-9
>Found 32 Calibration-10
>Found 512 Empty
>Found 288 Buffer
>Found 0 No data
>Found 32 Human Cot
>Found 32 Mouse Cot
>Found 32 B Actin
>Found 32 Poly A
>Found 32 Salmon Sperm
>Setting attributes: values Color
> > plotMA(RG)