[BioC] SpotTypes doesn't match

kevin Lin khlin at odin.mdacc.tmc.edu
Tue Sep 6 21:47:22 CEST 2005

Hi BioC,

I am using Limma, the problem occurs in my 2nd object RGgpr$genes$Status.

>  SpotTypes
   SpotType controltype Name  color
1  cDNA           *        *         black
2  genes       FALSE    *         grey
3  positive    positive    *         blue
4  ignore      ignore      *         orange
5 notprobe    notprobe  0         yellow

>  RGgpr$genes$Status <- controlStatus(SpotTypes, RGgpr$genes)
Matching patterns for: Name
Found 11592 cDNA
Found 11592 genes
Found 11592 positive
Found 11592 ignore
Found 664 notprobe
Setting attributes: values controltype color

I cut and pasted two columns (Name and controltype) of *.gpr files to 
confirm the different numbers of controltypes.
FALSE   ignore notprobe positive
   8564     2112      664      252

Q1, Why did they give me the same # 11592 ? Is it because I used wild 
card "*" ? Can this be fixed?
Q2, If so, what can i do with the SpotType.txt to fixed the problem ?

Thanks for any help


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