Hello,

I have a few general questions about custom CDFs. I believe that I
have created a custom cdf environment by removing specific probes from
the current environment.

I did so using a previous post

http://article.gmane.org/gmane.science.biology.informatics.conductor/4258/match=


I can see that an affybatch object reflects
the modification of the cdf. My problem is that I don't understand how
to save this environment for future use. In fact I do not have a cdf
file for the cdf that I have created.


when I do this:
newcdf <- wrapCdfEnvAffy(hgu133plus2cdf,1164,1164,"hgu133plus2cdf")

I get an error
Error in as.environment(from) : invalid object for 'as.environment'

The wrapCdfEnvAffy function creates a CdfEnvAffy object and then seems
to work OK until it gets to:

valid <- validCdfEnvAffy(object, verbose = verbose)


The following is the result of: print (object)

I believe it is the - in HG-U133_Plus_2 which causes the object to be
invalid. I am not sure what to do to get around this problem. I read a few
of the tutorials on the subject but I must be missing the answer.

Any ideas would be appreciated.


An object of class "CdfEnvAffy"
Slot "envir":
<environment: 0x112e3ab8>

Slot "envName":
[1] "HG-U133_Plus_2"

Slot "index2xy":
function (object, i)
{
    indices2xy(i, nr = object@nrow) - getOption("BioC")$affy$xy.offset
}

Slot "xy2index":
function (object, x, y)
{
    o <- getOption("BioC")$affy$xy.offset
    xy2indices(x + o, y + o, nr = object@nrow)
}

Slot "nrow":
[1] 1164

Slot "ncol":
[1] 1164

Slot "probeTypes":
[1] "pm" "mm"

Slot "chipType":
[1] "HG-U133_Plus_2"


Thanks for reading.

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