microarray , R package oligo and summarised level

Question

[chimerajit]

I am using R package oligo for microoarry analysis. In oligo user guide I found that oligo can summarise an exon array in 3 possible options; i.e. core, full, and extended. I like to know

1. what basis these 3 summarisation work?
2. what is possible logic I need to select one of them? or it is just my wish?

Answer 1

[cpad0112]

https://www.affymetrix.com/support/help/exon_glossary/index.affx Please read Related probe sets section.

[chimerajit]

thanks for your answer.

Answer 2

[Kevin Blighe]

Another answer: It's about how one 'summarises' the expression across one or more probes / probe-sets. In most cases, you will want 'core'. I have given answers on this:

• Human Exon array probeset to gene-level expression
• How to map probeset associated statistics to gene statistics in microarray differential expression analysis?

The choice is up to you about which to use.

Kevin