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

Memon, Farhat N fnmemo at essex.ac.uk
Mon Jan 18 15:56:28 CET 2010

Reference:  https://stat.ethz.ch/pipermail/bioconductor/2006-September/014242.html


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", "121_at:268:273")

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.


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