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

[Steve Lianoglou]

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