[BioC] FW: Problem in masking individual probes to calculate expression values

Jenny Drnevich drnevich at illinois.edu
Tue Jan 26 16:43:01 CET 2010

Hi Memon,

RemoveProbes() requires the probe name, in the format of 117_at1 or 
117_at9, not the x,y coordinates. I'm not sure there's an easy way to 
get from x,y coordinates to probe names, but some combination of 
indexProbes() and indices2xy() should work. You'll need an AffyBatch 
object of the raw data to test it, called "rawdata" in my code below.

 > x <- unlist(indexProbes(rawdata,genenames="117_at"))
 > x     # this will give you the indices of the pm probes for probe 
set 117_at along with their names

 > y <- indices2xy(x, abatch=rawdata)
 > y     # this will give you the x,y coordinates along with the 
correct probe names


At 08:56 AM 1/18/2010, Memon, Farhat N wrote:

>To calculate gcrma values of HG_U133_Plus_2 arrays, I am using Jenny 
>Drnevich's code (see the link above) (Thanks to Jim who provided 
>that link to me). This code is to mask either probesets or 
>individual probes while calculating gcrma values. I have 
>successfully run the code to mask some of the probe sets. Now, I 
>want to mask individual probes.
>For example, I want to calculate gcrma value of probe set 117_at 
>without a probe 60:815 and the probe set 121_at excluding three of 
>its probes 801:783, 228:969, 268:273 (the numbers are the 
>probes'  x:y positions).
>According to the code (in the above link), to call function 
>RemoveProbes(), I need to provide list of probe to be masked but it 
>is not mentioned in which format one should provide probe list.
>I used the following code that is not working:
>probe_list=c("117_at:60:815","121_at:801:783", "121_at:228:969", 
>cleancdf=cleancdfname("HG_U133_Plus_2", addcdf=FALSE)
>RemoveProbes(listOutProbes=probe_list, listOutProbeSets=NULL, cleancdf)
>I am getting error while masking probe. If anybody used this code to 
>mask individual probes, please let me know the format of the probe list.
>Thanks for your help in advance.
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>Search the archives: 

Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at illinois.edu

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