[BioC] modify CDF file for array study

[Hooiveld, Guido]

Hi Hyuna,

I don't have experience with removing (masking) individual probes from a
probeset, but I have used the procedure described in the thread linked
to below to remove complete probesets from a CDF file. However, it is
mentioned that "listOutProbes" could be used to remove probes.

HTH,
Guido

http://article.gmane.org/gmane.science.biology.informatics.conductor/986
9
### The first part is just creating two ojects (ResetEnvir and
RemoveProbes) originally
### written by Ariel Chernomoretz and modified by Jenny Drnevich to
remove individual
### probes and/or entire probesets.

 
------------------------------------------------
Guido Hooiveld, PhD
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
Wageningen University
Biotechnion, Bomenweg 2
NL-6703 HD Wageningen
the Netherlands

tel: (+)31 317 485788
fax: (+)31 317 483342

internet:   http://nutrigene.4t.com
email:      guido.hooiveld at wur.nl


> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch 
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of 
> Hyuna Yang
> Sent: 30 October 2007 16:56
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] modify CDF file for array study
> 
> Dear All,
> 
> I am using affy array, and want to modify CDF file. For 
> example, instead of all probes in a probe set, I want to use 
> some of them.
> My naive approach was, read data files modify them, replace 
> the original data, and remake a package, install the modified 
> package, and following shows specifically what I did.
> 
> I am using brainarray CDF, but guess this does not matter. To 
> use this CDF I need 'mma2mmentrezgprobe' (containing map) and 
> 'mma2mmentrezgcdf'(location of each probeset).
> 
> i) I read the 'mma2mmentrezgprobe' under the 
> mma2mmentrezgprobe/data and remove some rows 
> (mma2mmentrezgprobe = mma2mmentrezgprobe[-c(1:2),], and save 
> it under the original directory (save(mma2mmentrezgprobem,
> file='mma2mmentrezgprobe/data/mma2mmentrezgprobe.rda'))
> 
> ii) remove corresponding rows in data ('mma2mmentrezgcdf') 
> under mma2mmentrezgcdf/data using assign and get; something 
> like this b = get(ls(mma2mmentrezgcdf)[1], mma2mmentrezgcdf) 
> ; b = b[-1:2,] ; assign(ls(mma2mmentrezgcdf)[1], b, envir = 
> mma2mmentrezgcdf) ; #then save this; save(mma2mmentrezgcdf, 
> file = ''mma2mmentrezgcdf/data/mma2mmentrezgcdf')
> 
> then make a package and install it again.
> (R CMD build mma2mmentrezgcdf; R CMD INSTALL mma2mmentrezgcdf;)
> 
> However, it does not work. It seems has problem in 
> ".next.method(e1, e2)"
> 
> I wonder if someone can help me to modify existing CDF file.
> 
> Thanks you,
> 
> 
> Hyuna
> 
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