Re: Reproducing RMA with Gene ST data (Was: Re: [aroma.affymetrix] Re: How do you analyze Gene ST Data?)

2008-12-30 Thread Andy_Paparountas
Hi all , I really find this conversation very interesting. I am trying to analyze a set of 3 treatment and 3 control samples of MoGeneSt10 array. Thus far with the code pwhite shared I was able to do RMA Background correction , quantile normalization and got QC , RLE , NUSE , density plots. Q1.

[aroma.affymetrix] Re: How do you analyze Gene ST Data?

2008-12-30 Thread Andy_Paparountas
And how about linking the annotation csv with the data.frame (normalized data)? Is there any possibility to use library(mogene10st.db) and library(annaffy) ? to report the normalized data with the associated annotations? It would really help to have some related code Thanks On 26 Νοέ,