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$genes)
>Matching patterns for: Name
>Found 11592 cDNA
>Found 11592 genes
>Found 11592 positive
>Found 11592 ignore
>Found 664 notprobe
>Setting attributes: values controltype color
>
>I cut and pasted two columns (Name and controltype) of *.gpr files to
>confirm the different numbers of controltypes.
> >table(read.table("twoColumns.txt",sep='\t',header=F))
>FALSE ignore notprobe positive
> 8564 2112 664 252
>
>Q1, Why did they give me the same # 11592 ? Is it because I used wild
>card "*" ? Can this be fixed?
>Q2, If so, what can i do with the SpotType.txt to fixed the problem ?
>
>Thanks for any help
>
>Kevin
If you type
names(RGgpr$genes)
you will see that there is no column called 'controltype' in the
annotation
component your data object. The problem is that 'controltype' is not a
standard GenePix annotation column. Hence limma will not know to read
it in
unless you tell it to by including this column in the 'annotation'
argument
of read.maimages(). That is, you need to use
RGgpr <- read.maimages(..., annotation=c("Name","controltype"))
Gordon
>To: kevin Lin <khlin at="" odin.mdacc.tmc.edu="">
>From: Gordon Smyth <smyth at="" wehi.edu.au="">
>Subject: [BioC] SpotTypes doesn't match
>Cc: bioconductor at stat.math.ethz.ch
>Date: Thu, 08 Sep 2005 10:30:21 +1000
>
>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