[BioC] limma spottype

[James W. MacDonald]

Hi Assa,

On 8/1/2012 9:29 AM, Assa Yeroslaviz wrote:
> Hi User,
>
> I am trying to plot my M-A levels using different colors for the controls.
> For that I created a spottype file, which looks like that:
> SpotType    ControlType    Color
> gene    0    black
> NC    -1    green
> PC    1    red
>
> In my agilent files I don't have columns named "ID" or "Name", But I can
> sperate my controls with the ControlType column. This I also read in the
> the read.maimages() annotations.
>
> This is how I run the analysis (agilent two-color arrays)
>
>> targets<- readTargets("targets.txt")
>> SpotTypes = readSpotTypes()
>> RG<- read.maimages(targets, path="rawData", columns = list(G =
> "gMedianSignal", Gb = "gBGMedianSignal", R = "rMedianSignal",
>     Rb = "rBGMedianSignal"), names = targets$Cy5, annotation = c("Row",
> "Col","FeatureNum", "ControlType","ProbeName", "GeneName") )
> RG$gene$Status = controlStatus(SpotTypes, RG)
>   to check the results of that I did:
>> table(RG$gene$Status)

I believe you want RG$genes$Status.

Best,

Jim

>   gene    NC    PC
> 43096   555  1563
>
> But even than I don't see any controls in my plot. Everything is black.
> Do I do anything wrong?
>
> Is there another way to color different groups?
>
> Thanks
> Assa
>
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>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099