Entering edit mode
Hyuna Yang
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10
@hyuna-yang-2463
Last seen 10.3 years ago
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
