[BioC] probe masking

[Donna]

James MacDonald <jmacdon at ...> writes:

> 
> Hi Donna,
> 
> See the function posted by Jenny Drnevich about half way down this post:
> 
>
http://article.gmane.org/gmane.science.biology.informatics.conductor/9887/match=probe+mask
> 
> Best,
> 
> Jim
> 
> Donna Toleno wrote:
> > Hello,
> > 
> > I am looking for an answer which I believe has been discussed on the list
previously. I would like to know how
> to modify the cdf environment in order to mask out certain probes for a
between species analysis.


Thank you for your reply Jim. It has been very helpful. I was able to remove the
unwanted "masked" intensity data by changing the appropriate intensity values to
NA. Then I found that this is not a solution to my problem because RMA will not
accept NA values. So I'm back to modifying the cdf. 

I used the code you pointed me to as well as some related code posted by Ariel
Chernomoretz. When I try things line by line, I have found that there is still a
problem with the following line:


> a<-get(pset[i],env=get(cdfpackagename))
Error in get(x, envir, mode, inherits) : invalid 'envir' argument


> cdfpackagename
[1] "mouse4302cdf"
> pset[i]
[1] "1448591_at"

I wonder what the following lines are for?

     #a<-get(pset[i], env=get(cdfpackagename))
     #a<-a[-iout,]
     #assign(pset[i],a,env=get(cdfpackagename))

I thought that I could at least remove the whole probesets without the above
problematic lines.

so when I try

> rm(list=listOutProbeSets,envir=get(cdfpackagename))

I get a similar error.

Error in remove(list, envir, inherits) : invalid 'envir' argument

So I guess my question is what is the valid environment argument?

> listOutProbeSets
[1] "1415897_a_at" "1434465_x_at" "1439066_at"  

Could the problem be due to syntax differences. I am using R and Bioconductor on
Windows?
I made a few syntax changes already including a change from "xy2i" to
"xy2indices" based on an error message. Unfortunately, the help files for rm and
for get were not very helpful.

Any comments would be appreciated.

Thanks,

Donna