[BioC] a modified cdf environment

[James W. MacDonald]

Hi Donna,

Donna Toleno wrote:
> 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.

Not sure what you mean by a cdf file. The environment you have created 
is sitting in your .GlobalEnv, which is really just your R workspace. If 
you quit R and save the workspace, then the environment will be there 
when you restart R in that directory (or restart R elsewhere, and then 
load() that workspace). This is the easiest way to save things.

You could also make a package containing the environment, but that will 
take more work. If you really want to do this, take a look at the 
make.cdf.package() function in makecdfenv. You won't be able to use this 
function directly -- instead you will have to run the relevant portions 
(probably from 'symbols' on down, although I would have to try myself to 
know for sure).

Best,

Jim


> 
> 
> 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 at 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 at nrow)
> }
> 
> Slot "nrow":
> [1] 1164
> 
> Slot "ncol":
> [1] 1164
> 
> Slot "probeTypes":
> [1] "pm" "mm"
> 
> Slot "chipType":
> [1] "HG-U133_Plus_2"
> 
> 
> Thanks for reading.
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623