R help - Oct 2004 - Help with Affymetrix data

I have CEL files from Affymetrix Mouse Array 430_2 and am trying to get the 
the individual PM intensities (11 per gene) for each sample. I would like to 
write out this into a tab delimited text file. Where am I stalling? This is 
what I've done:

Change dir(to where CEL files are saved)
Data <- ReadAffy()
eset <- rma(Data)
write.exprs(eset, file="mydata.txt")

With this I am only able to get the average intensities per gene not the 
intensity per probe of each gene.

Please help me out.

Kanan

use PM function in Affy package.

Frank


On Mon, 4 Oct 2004 16:48:12 -0400, kvyas <kvyas at utk.edu>
wrote:
> I have CEL files from Affymetrix Mouse Array 430_2 and am trying to get the
> the individual PM intensities (11 per gene) for each sample. I would like
to
> write out this into a tab delimited text file. Where am I stalling? This is
> what I've done:
> 
> Change dir(to where CEL files are saved)
> Data <- ReadAffy()
> eset <- rma(Data)
> write.exprs(eset, file="mydata.txt")
> 
> With this I am only able to get the average intensities per gene not the
> intensity per probe of each gene.
> 
> Please help me out.
> 
> Kanan
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
>

I have made some progress.

Change dir(to where CEL files are saved)
Data <- ReadAffy()
eset <- rma(Data)
my.pm.data <- pm(Data)
write.table (my.pm.data, file = "pmprobes3.csv", sep = ",",
col.names = TRUE,
row.names = probeNames(Data))

This results in the following:

Probe	Sam1	Sam2	Sam3	Sam4
1415670_at01	340	383	376	320
1415670_at02	794	932	734	697
1415670_at03	1117	1366	1013	932
1415670_at04	97	97	148	94
1415670_at05	387	405	367	402
1415670_at06	485	553	391	343
1415670_at07	458	509	410	385
1415670_at08	507	684	616	545
1415670_at09	311	392	576	463
1415670_at10	691	822	688	588
1415670_at11	512	726	3201	2317
1415671_at01	1230	1212	873	770
1415671_at02	886	877	794	729
1415671_at03	1472	1682	1263	1152
1415671_at04	1171	1214	948	914
1415671_at05	390	479	435	396
1415671_at06	462	513	423	389
1415671_at07	987	1151	1102	815
1415671_at08	992	1066	1203	1013
1415671_at09	489	534	501	385
1415671_at10	401	509	379	293
1415671_at11	1443	1686	1410	1215


How can I get the p-value for each probe?


>===== Original Message From Frank Duan <fhduan at gmail.com>
====>use PM function in Affy package.
>
>Frank
>
>
>On Mon, 4 Oct 2004 16:48:12 -0400, kvyas <kvyas at utk.edu> wrote:
>> I have CEL files from Affymetrix Mouse Array 430_2 and am trying to get
the
>> the individual PM intensities (11 per gene) for each sample. I would
like
to
>> write out this into a tab delimited text file. Where am I stalling?
This is
>> what I've done:
>>
>> Change dir(to where CEL files are saved)
>> Data <- ReadAffy()
>> eset <- rma(Data)
>> write.exprs(eset, file="mydata.txt")
>>
>> With this I am only able to get the average intensities per gene not
the
>> intensity per probe of each gene.
>>
>> Please help me out.
>>
>> Kanan
>>
>> ______________________________________________
>> R-help at stat.math.ethz.ch mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide! 
http://www.R-project.org/posting-guide.html
>>