[BioC] modify CDF file for array study

[Michal Okoniewski]

 Hi Hyuna,

You can modify CDF to do experiments "on the fly" without
creating a metadata library. CDF is just an environment. So:

1) get the pre-installed CDF as an environment, eg:
library("exon.pmcdf")
my.env <- get("exon.pmcdf")

2) attach the CDF to your AffyBatch:
raw.data at cdfName <- "exon.pmcdf"

3) Modify the CDF as you wish. it consists of variables 
with names identical to probesets and the values are data
frame with "pm" and "mm" columns. So you can do, eg:

assign("2315108",rbind(get("2315108", envir=my.env),get("2315108",
envir=my.env)),env=my.env)

This example merges probes from two probesets into one. You can use
get(), assign(), rm() etc 
to play around with the CDF environment. 

4) Run the summarization and interpret it according to your beliefs and
intuitions ;)

5) Once you are happy with the CDF environment you may save it for good
using makecdfenv package. 

Have fun, 
Michal 

-----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 15:56
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

_______________________________________________
Bioconductor mailing list
Bioconductor at stat.math.ethz.ch
https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor

--------------------------------------------------------


This email is confidential and intended solely for the u...{{dropped:13}}