[BiO BB] Re: question about Agilent microarray data format

[Xiaowei JIANG]

 Dear,

I asked the same question to the group weeks ago.
I used the raw Agilent microarray data in the JMP Microarray  analysis
platform. I did data preprocessing , normalization , gene selection,
multidimensional scaling , PCA , clustering ananysis , and annotation
analysis on the same platform 

The data input engine of JMP Micoarray used the columns  "gProcessedSignal"
and  "rProcessedSignal" to produce the SAS data set, I used a log2
transformation to make the data more normal like.  Depending on your
experiment and design, you choose your specific normalization method, there
are some books talking about this situation. So you need specific
normalization softwares, and other analysis platforms to perform data
preprocessing and data analysis.

So for the Agilent data format , you dont actually need to care too much
about the data format itself, instead, you should consider more about the
preprocessing and data analysis methods you are going to use , the whole
analysis procedure pertaining to the streamlined analysis software platforms
should be considered in advance, etc. 


Kind regards,
Xiaowei JIANG