[aroma.affymetrix] Extracting probe level intensities

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San
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[aroma.affymetrix] Extracting probe level intensities

San
Hi,

I was wondering if its possible to extract probe level intensities from cel files without depending on a particular CDF file? 

At the moment I am using:

df <- readDataFrame(getCdf(cs), verbose=-80)
raw<-extractMatrix(cs,cells=df$cell,verbose=verbose)


But its dependent on the CDF file thus we will only have probes that are included within the CDF. However we want the intensities for all probes irrespective of the CDF used.

Is this possible in aroma.affymetrix?

Regards,
Sanj




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Re: [aroma.affymetrix] Extracting probe level intensities

Henrik Bengtsson-4

Hi,

just exclude argument 'cells', i.e.

data <- extractMatrix(cs)

This will reads all cells/probes.

Henrik

On Mar 2, 2016 05:47, "sanj" <[hidden email]> wrote:
Hi,

I was wondering if its possible to extract probe level intensities from cel files without depending on a particular CDF file? 

At the moment I am using:

df <- readDataFrame(getCdf(cs), verbose=-80)
raw<-extractMatrix(cs,cells=df$cell,verbose=verbose)


But its dependent on the CDF file thus we will only have probes that are included within the CDF. However we want the intensities for all probes irrespective of the CDF used.

Is this possible in aroma.affymetrix?

Regards,
Sanj




--
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.
 
 
You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to [hidden email]
To unsubscribe and other options, go to http://www.aroma-project.org/forum/

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--
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.
 
 
You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to [hidden email]
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