Hi Assa,

here is what I want to do:

- get the raw intensities values (as exprs object) of affybatch object
(reading from the raw data direxctly), along with the probe IDS
- get the normalized intesity values of the affybatch object
- Compare the intesities between the two generated results by looking at
the probe intensity values

The code you sent me produced duplicate probe values, see below:

          affyIDs AFX_1_A1.CEL AFX_1_A2.CEL AFX_1_A3.CEL AFX_1_A4.CEL
369707  1007_s_at          200          201          208          202
563318  1007_s_at          398          491          425          464
1049349 1007_s_at          427          547          528          446


I already tried something simple:

data<-ReadyAffy()
expr <- exprs(data)
eset <- new("ExpressionSet", exprs = expr, phenoData = pheno)

Still the probe IDS are missing for the eset object.


Can anyone help me on how to extract raw intensity values from an affy
object.

regards,
Shweta
---------- Forwarded message ----------
From: Assa Yeroslaviz <frymor@gmail.com>
Date: Mon, Jan 6, 2014 at 11:42 AM
Subject: Re: Help needed: extracting raw intensity values from Affy
To: shweta bagewadi <bagewadi.shweta@gmail.com>


Hi,

here is something I did for my arrays.
It depends what kind of arrays you are using.

Data<-ReadAffy(celfile.path="path to your arrrays" ,filenames="Name of
files" phenoData="Phenodata", verbose=TRUE)
mypm <- pm(Data) # Retrieves PM intensity values for single probes
mymm <- mm(Data) # Retrieves MM intensity values for single probes
affyIDs <- probeNames(Data) # Retrieves Affy IDs
result <- data.frame(affyIDs, mypm, mymm) # Combines the above information
in data frame


Hope this is helping

cu,
Assa

PS.

please write to the forum (put the person than on cc), as I am sure you'll
will get help much faster.



On Mon, Jan 6, 2014 at 10:35 AM, shweta bagewadi
<bagewadi.shweta@gmail.com>wrote:

> Hi,
>
> I saw in BioC blog that u have created a thread on hopw to extract raw
> intensity values from affy object. I am also trying to do the same.
> Unfortunately, I do not see any solution in this thread.
>
> Did you find a solution for it? If yes, could you please guide me how you
> did it.
>
> Thanlks in advance.
>
> --
> Regards,
> Shweta
>




-- 
Regards,
Shweta

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