[BioC] Z-Score Calculation for hgu133plus2 affymetrix microarray.

[Matthew McCall]

Murtuza,

I can't speak to the BioGPS website, but the reason you are getting an
error is that you are trying to run the frma function on the bcparams
matrix. As the error message says, the object passed to the frma
function must be an AffyBatch or ExonFeatureSet.

Looking at the example:
library(frmaExampleData)
data(AffyBatchExample)
object <- frma(AffyBatchExample)

Here AffyBatchExample is an AffyBatch, so the call to frma works.

As for the z-scores, just pass output="z-score" to the barcode function.

All of this (and more) is explained in the vignette for the frma package:
http://bioconductor.org/packages/2.9/bioc/vignettes/frma/inst/doc/frma.pdf

Best,
Matt

On Sat, Feb 4, 2012 at 12:13 PM, Steve Lianoglou
<mailinglist.honeypot at gmail.com> wrote:
> Hi Martuza,
>
> On Fri, Feb 3, 2012 at 5:18 PM, Murtuza Zair <mzair at uhnresearch.ca> wrote:
>> Hi,
>> I am trying to replicate the data on biogps.com of the Z-score.
>
> I guess you mean biogps.org, no?
>
>> They explain
>> the source of how they calculated it.
>
> Can you give us a link to the precise tutorial/faq/whatever you are
> referring to?
>
>> and have been struggling to run the following code...
>>
>> 6. Read in the data and preprocess using the default options.
>>> library(frmaExampleData)
>>> data(AffyBatchExample)
>>> object <- frma(AffyBatchExample)
>> 7. Create a gene expression barcode.
>>> bc <- barcode(object)
>>
>> I have gotten to the point of data(bcparams).. which runs fine...
>>
>> However, object <- frma(bcparams) ... I get an error message...
>>
>> "Error in frma(bcparams) :
>>  object must be of class AffyBatch or ExonFeatureSet"
>>
>> Please help with this step... as well, I am not interested in the barcode
>> but the z-score... how would I output this...
>
> As I mentioned above, you'll have to give a direct link to whatever it
> is that you are trying to follow along to if you want any real help.
>
> Calculating the z-score of a matrix is pretty much what the base R
> `scale` function does, so ... performing the calculation itself is
> rather straightforward.
>
> -steve
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
>
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-- 
Matthew N McCall, PhD
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