[BioC] modify CDF file for array study

[Hyuna Yang]

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