[BioC] RE: [R] Help with Affymetrix data

[kvyas]

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
>>
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