[BioC] limma and spottypes

[Simon Melov]

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?

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)
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