Question: How to create vectors (makeVectorsAffyBatch) , using own cdf
0
gravatar for osieman52
12 months ago by
osieman520
osieman520 wrote:

Dear Matthew (or anyone that can help me),

I am trying to create my own vectors using frmaTools. Therefore I am also using a custom cdf enviroment. But somehow I receive error's trying to create the vector. I'm sure that I use the "cdfname" the wrong way but can't find any examples on how to use it probarly.

I used it this way:

newVecs <- makeVectorsAffyBatch(files = CelFilenames, batch.id = rep(1:200, each = 5) ,cdfname = "hgu133plus2sharedprobescdf", verbose = TRUE)`

The hgu133plus2sharedprobescdf is an enviorement, that works if I use it for the function :

readAffy( "file.CEL" ,cdfname= "hgu133plus2sharedprobescdf") 

I receive the following error:

Error in packageVersion(cdfname) : 
package 'hgu133plus2sharedprobescdf' not found
Calls: makeVectorsAffyBatch -> packageVersion
Execution halted

Some how it can't find the package I load in, or I am using it the wrong way. 

I hope that someone can help me out with this.

Thanks in advance!

Osman

 

 

ADD COMMENTlink modified 12 months ago by Matthew McCall830 • written 12 months ago by osieman520
Answer: How to create vectors (makeVectorsAffyBatch) , using own cdf
1
gravatar for Matthew McCall
12 months ago by
United States
Matthew McCall830 wrote:

The error message is telling you that it is looking for the package version of your cdf and not finding one. This is likely because you created the cdf environment but not a package. makeVectorsAffyBatch wants a package so that it can check that when you run frma on new data it was read in using the same version of the same cdf. This was done to increase reproducibility and encourage those who develop new frmavectors to share their work with others via a package.

ADD COMMENTlink written 12 months ago by Matthew McCall830

I see.what would you suggest me to do in order the fix this, because I would like the use this cdf since it has the probes I'm interested in. Is there a way to convert it in to a package so that `makeVectorsAffyBatch` can accept it or is there another way to do this.

Thanks in advance!

ADD REPLYlink modified 12 months ago • written 12 months ago by osieman520
1

You would create an R package in the standard way. See for example: 

Hadley Wickham's book: http://r-pkgs.had.co.nz/

And the BioC package guidelines: http://bioconductor.org/developers/package-guidelines/

Also any of the current frmavecs packages can serve as a useful template. 

ADD REPLYlink written 12 months ago by Matthew McCall830
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