[BioC] Extracting data sub set from loaded data.

[elliott harrison]

Hi Jim, 
Thanks for the reply (and to all those who replied).
I understand what you are telling me to do (I think) but am having
trouble achieving it.

I got a list of probes from my full data set like this.
RPL = R$genes[6]
44998     A_23_P90369
44999     A_32_P38745
45000    A_24_P246406
45001      A_23_P5757
45002    A_24_P926284
45003      A_23_P1331
45004    A_23_P164289

I've loaded my interesting probes like this.
b=read.csv("600probes.txt", sep="\t", header=T)
b
586 A_23_P337726
587 A_23_P251095
588 A_24_P277934
589 A_23_P205499
590  A_23_P85236
591 A_24_P335202
592 A_23_P203920
593 A_24_P146211

I've tried to match the 2 lists
> vec <- match(b, RPL)
> vec
[1] NA
Match against the main data set
> vec <- match(b, R)
> vec
[1] NA
Match against the corresponding value in the data set
> vec <- match(b, R$Genes[6])
> vec
[1] NA

I'm missing something obvious I know but a little more nudging would be
appreciated.

Many Thanks

Elliott


 

-----Original Message-----
From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
Sent: Wednesday, October 24, 2007 4:21 PM
To: elliott harrison
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Extracting data sub set from loaded data.

Hi Elliott,

elliott harrison wrote:
> Dear BioC,
> 
> I'm drawing a blank on the archives but I'm sure someone can help 
> point me to the right place.
> I have raw data from Agilent whole genome array in R in a dataset (RG)

> imported using  read.maimages.
>>From analysis in a different software I have a list of probes I wish 
>>to
> analyse independently.
> How do I load the list of probes into R and then use it to extract 
> data from my loaded data and create a new dataset?
> Or do I have to reload the data with just the probes I'm interested
in?

According to the help file for subsetting in limma (accessed either via
help.start() or ?"[.RGList"), you can subset an RGList just like
anything else. Something like

newRGList <- fullRGList[theprobevector,]

should work. Alternatively you could extract the probe names from the
RGList and then use match() to get a numeric vector.

vec <- match(theprobevector, allprobes)
newRGList <- fullRGList[vec,]

Apparently you can also convert to an exprSet (I assume now you can
convert to an ExpressionSet, but Gordon will have to comment on that
possibility), which also has capabilities for subsetting via a vector of
probe names.

Best,

Jim


> 
> Many Thanks
> 
> Elliott
> 
> 
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--
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


 


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