[BioC] some basic questions

[anand mt [guest]]

Hi all..

i have following questions.

1) How many probesets represent a gene on microarray chip ?

2) How do i access raw intesity value of probes (before normalization) ?

3) Do i need to read cdf file to do that ??
 
4) After pre-processing the data and normalization, we generally go for significance tests and gene grouping. My question is, if i group the genes before performing  significance test (say now i have 3 groups based on apoptosis,cell cycle, DNA replication) and then perform significance test within each group, will the results be same as that of conventional way ?? Is it a valid method to do so??

Sorry if my questions are silly.

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