[BioC] Subsetting data from RGList (Again)

[elliott harrison]

Hi All, 
Sorry to trouble everyone  but I didn't get my subsetting of an RGList
sorted last week.
I've tried loads of different combinations of things that were suggested
but not quite there yet.

MY Data is an RGList object here is a bit
> R[1,1]
An object of class "RGList"
$G
     C:\\Program Files\\Agilent\\GeneSpring
GX\\data\\CRX\\980\\test01_251485020980_S01_GE2-v5_91_0806_2_1_1
[1,]
15662.69
 
$Gb
     C:\\Program Files\\Agilent\\GeneSpring
GX\\data\\CRX\\980\\test01_251485020980_S01_GE2-v5_91_0806_2_1_1
[1,]
73.9323
 
$R
     C:\\Program Files\\Agilent\\GeneSpring
GX\\data\\CRX\\980\\test01_251485020980_S01_GE2-v5_91_0806_2_1_1
[1,]
15662.69
 
$Rb
     C:\\Program Files\\Agilent\\GeneSpring
GX\\data\\CRX\\980\\test01_251485020980_S01_GE2-v5_91_0806_2_1_1
[1,]
73.9323
 
$weights
     C:\\Program Files\\Agilent\\GeneSpring
GX\\data\\CRX\\980\\test01_251485020980_S01_GE2-v5_91_0806_2_1_1
[1,]
0
 
$targets
  SlideNumber   Name
FileName Treatment MasterTreatment
1        9801 Pre1_1 C:\\Program Files\\Agilent\\GeneSpring
GX\\data\\CRX\\980\\test01_251485020980_S01_GE2-v5_91_0806_2_1_1.txt
Pre1             Pre
       Cy3 Cy5       Date
1 WildType Ref 11/09/2007
 
$genes
  Row Col FeatureNum ProbeUID ControlType       ProbeName
GeneName  SystematicName   Status
1   1   1          1        0           1 GE_BrightCorner
GE_BrightCorner GE_BrightCorner Control6
 
$source
[1] "generic"
 
 
My list of probes to select data with is in this object.
> a
           Gene.Probe
Probe1   A_24_P329635
Probe2   A_23_P104098
Probe3   A_23_P419038
Probe4   A_24_P124550
Probe5    A_23_P99044
 
 
 
 
I've tried
A=rownames(a)
RA = R[A,]
 
But don't get any genes
>$genes
[1] Row            Col            FeatureNum     ProbeUID
ControlType    ProbeName      GeneName       SystematicName Status

<0 rows> (or 0-length row.names)
 
I've tried creating a vector using match a load of different ways but it
is always empty
>vec = match(A, R)
>vec = match(A, R$genes$ProbeName)
>vec = match(A, R$genes)
>vec = match(probelist600, R)
>vec = match(probelist600, R$genes)
>vec = match(probelist600, R$genes$ProbeName)
 
 
This is part what ends up in object A
> A
  [1] "Probe1"   "Probe2"   "Probe3"   "Probe4"   "Probe5"   "Probe6"
"Probe7"   "Probe8"   "Probe9"   "Probe10"  "Probe11"  "Probe12"
"Probe13" 

I expected to see my probe names in there.
I'm clearly not getting something. 
Can anyone see where I'm going wrong?
Many Thanks
Elliott


This message has been scanned for viruses by BlackSpider...{{dropped:3}}