[BioC] how to get probe ids??

[anand m t]

Hi all..

I'm very new to microarray analysis.
i've been given two datasets for analysis. (experimental and control
with 3 replicates each)
I've encountered following errors/problems..

1.whenever i tried to run mas5calls, it throws an error saying the
presence of NA/Inf/NAN's in the data.

> affy.data=ReadAffy()
> data.mas5calls = mas5calls(affy.data)
Getting probe level data...
Computing p-values
Error in FUN(1:6[[1L]], ...) :
  NA/NaN/Inf in foreign function call (arg 2)

then i tried removing NA's using following command..

> na.omit(affy.data)
AffyBatch object
size of arrays=1050x1050 features (18 kb)
cdf=MoGene-1_0-st-v1 (35556 affyids)
number of samples=6
number of genes=35556
annotation=mogene10stv1
notes=

But even after, the same problem exists. How do i solve this??

2. I skipped this step and proceed with next step. I calculated
p-values and extracted all statistically significant probes. But,
look at my probe names (rma normalized data)

probe_names	control_1	control_2	control_3	experimental_1	experimental_2	experimental_3
10338001	11.70433113	11.09411799	11.17114406	12.3810603	11.3593078	11.30987883
10338002	7.455822379	7.022795366	6.977515221	7.863429983	6.659503501	6.583122799
10338003	9.944000269	9.329330062	9.439069933	10.87092521	9.507433404	9.421644356
10338004	8.807458574	8.190795944	8.336526249	9.666564028	8.555489147	

It doest have any probe extensions such as "_at", etc.  what might be
the problem?? How do i proceed now ??
-- 
******************************************************************
Anand M.T
School of Biotechnology (Bio-Informatics),
International Instituteof Information Technology (I2IT),
P-14, Rajiv Gandhi Infotech park,
Hinjewadi,
Pune-411 057.
INDIA.

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