[BioC] SpotTypes doesn't match

[Gordon Smyth]

I suspect you will find that there is no column called "controltype" in 
your GPR files. Perhaps check the capitalisation.

Gordon

>Date: Tue, 6 Sep 2005 14:47:22 -0500
>From: kevin Lin <khlin at odin.mdacc.tmc.edu>
>Subject: [BioC] SpotTypes doesn't match
>To: <Bioconductor at stat.math.ethz.ch>
>Message-ID: <a06002001bf439982ab56@[143.111.133.119]>
>Content-Type: text/plain; charset="us-ascii" ; format="flowed"
>
>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.
> >table(read.table("twoColumns.txt",sep='\t',header=F))
>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
>
>Kevin