[BioC] Question about affy

[Deepayan Sarkar]

Hi,

I'm using the affy package to read in data from 6 MG_U74A chips. 
This is my first time, so I'm trying to replicate the steps in 
affy.pdf. The data seems to be read in properly, and pm, mm, 
boxplot, normalize all seem to work on the whole object. 

However, any attempt to take subsets of the object itself fails:

> Data <- ReadAffy()
> Data[1,]
Error in checkSlotAssignment(object, name, value) : 
	Value supplied is not valid for slot "pData", is(value, "data.frame") is not
TRUE
> Data[,1]
Error in checkSlotAssignment(object, name, value) : 
	Value supplied is not valid for slot "pData", is(value, "data.frame") is not
TRUE

Any pointers on what might be causing this ?

Deepayan

----------------------------------------------------
P.S.: In case it helps, here's some more output:


> Data <- ReadAffy()
reading CDF file
processing information
reading 6 CEL files......
preparing probe level object


> Data
Plob object
CDF used=MG_U74A.cdf
number of chips=6
number of genes=12654
number of probe pairs=201964
annotation=
description=
notes=
size of chip=640x640
chip names=
aged0-1
aged0-2
aged0-3
young0-1
young0-2
young0-3


> pm(Data)[1:5,]
             aged0-1 aged0-2 aged0-3 young0-1 young0-2 young0-3
97180_f_at12 15687.0 14791.0 17047.0  15903.8  16362.0  13671.0
97368_at10   18634.0 14839.3 19023.0  18568.0  20432.0  16068.0
97579_f_at8   5508.8  5069.8  5572.8   6346.0   7474.5   5642.5
95664_at5     6101.0  4624.3  6912.0   7200.0   7652.0   6821.0
101287_s_at5  1526.0  1336.3  1505.0   1993.0   1835.0   1774.0


> mm(Data)[1:5,]
             aged0-1 aged0-2 aged0-3 young0-1 young0-2 young0-3
97180_f_at12 10309.8 10016.0 10891.0  13610.3  13646.0  11988.0
97368_at10    6745.3  5097.0  6346.3   9579.0   7937.0   6944.0
97579_f_at8   3165.5  2809.0  3509.8   4360.0   4396.3   3580.8
95664_at5     3557.0  2729.0  3972.5   5056.5   4385.0   4197.0
101287_s_at5   962.8   836.8  1059.5   1294.0   1160.0   1492.0





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