[BioC] How to remove some probes from one probeset in the begining?

[pkuonline]

Hi Wolfgang,

Many thanks for your rapid reply. 

Your code appears to work!

Best regards,
-------------------------------------------------------------
Yong Zhang
Ph.D, Research Scholar
Manyuan Long's Lab
University of Chicago

-------------------------------------------------------------
From: Wolfgang Huber
Time: 2008-03-03 11:02:55
To: pkuonline at gmail.com  bioconductor
Subject: Re: [BioC] How to remove some probes from one probeset in the begining?

03/03/2008 04:42 pkuonline scripsit
> Dear All,
> 
> Taking HG-U133_PLUS_2 as an example, one probeset consists of 11 individual probes. I'd like to exclude few non-specific probes from one probeset for genes of interest before the subsequent all analysis. I searched the Archive. It seemed I need to generate a customized CDF file. I am just wondering whether there are some relatively simple methods. If not, could someone show how to modify the pre-existing HG-U133_PLUS_2 CDF file to exclude few probes? 
> 
> Many thanks ahead.
>  				
> Best regards,
> -------------------------------------------------------------
> Yong Zhang
> Ph.D, Research Scholar
> Manyuan Long's Lab
> University of Chicago
> 
Dear Yong

suppose you want to remove the 4-th probe in probeset 1552391_at, then
the code would be about as follows. You will need to do this after
attaching the hgu133plus2cdf package and before calling functions like rma.


> library("hgu133plus2cdf")
> ls(hgu133plus2cdf)[100]
[1] "1552391_at"
> hgu133plus2cdf$"1552391_at"
           pm      mm
 [1,]  618104  619268
 [2,]  216159  217323
 [3,]  353306  354470
 [4,]  165282  166446
 [5,]  658545  659709
 [6,]  704429  705593
 [7,]  867194  868358
 [8,]  541423  542587
 [9,]  932914  934078
[10,]  362488  363652
[11,] 1002956 1004120
> hgu133plus2cdf$"1552391_at" =  hgu133plus2cdf$"1552391_at"[-4,]
> hgu133plus2cdf$"1552391_at"
           pm      mm
 [1,]  618104  619268
 [2,]  216159  217323
 [3,]  353306  354470
 [4,]  658545  659709
 [5,]  704429  705593
 [6,]  867194  868358
 [7,]  541423  542587
 [8,]  932914  934078
 [9,]  362488  363652
[10,] 1002956 1004120


> sessionInfo()
R version 2.7.0 Under development (unstable) (2008-03-02 r44660)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=it_IT.UTF-8;LC_NUMERIC=C;LC_TIME=it_IT.UTF-8;LC_COLLATE=it_IT.UTF-8;LC_MONETARY=it_IT.UTF-8;LC_MESSAGES=it_IT.UTF-8;LC_PAPER=it_IT.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=it_IT.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] hgu133plus2cdf_2.0.0 fortunes_1.3-4

loaded via a namespace (and not attached):
[1] tools_2.7.0


-- 
Best wishes
 Wolfgang

------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber