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J-Express => Forum => Topic started by: jnuxz on June 28, 2006, 08:11:05 AM



Title: How to analyse the data from agilent microarray?
Post by: jnuxz on June 28, 2006, 08:11:05 AM
I can't analyse the data from agilent microarray by the J-E directly. Since the date form of agilent is different from that of affymetrix.

Is it necessary that the date from the agilent scanner should be normalized or modifized before J-E analysis? and how to do it? i can't get it from the manual provided. 


Title: Re: How to analyse the data from agilent microarray?
Post by: Bjarte Dysvik on June 29, 2006, 11:47:54 AM
Agilent microarray data can be loaded using the SpotPix Suite (select load raw data from the file menu),

If the Files are in a known format, it should be enough just to drag and drop the files from your file explorer to the "Samples" table in spotpix suite.
See more about this in the tutorial "loading image quantitation data" installed together with J-Express. In this document you can also find information about how to filter and normalize your data.


bjarte


Title: Re: How to analyse the data from agilent microarray?
Post by: eivindfi on March 13, 2008, 12:46:45 PM
Quote
See more about this in the tutorial "loading image quantitation data" installed together with J-Express. In this document you can also find information about how to filter and normalize your data.

I can't find any tutorial named "loading image quantitation data". Maybe this has been changed and put somewhere else? I am also curious about normalization and filtering of Agilent data, but I suspect that Agilent will have to answer this?


Title: Re: How to analyse the data from agilent microarray?
Post by: Bjarte Dysvik on March 13, 2008, 10:14:54 PM
The document should be installed together with J-Express. If you use windows it should be in the start-group together with the shortcut to the J-Express executable. Anyway, the document is also available from www.molmine.com/jexpress/doc.

I know there are many groups loading Agilent data into petrel. Perhaps someone wants to share their experience and best practices?