I used 45K rice slide in my experiment and need to analyze the data using limma package in bio-conductor. Can anyone lend advice on this topic? Does anyone have experience with the GUI bio-conductor? Is there a better way to analyze this data?
limma package is one of the best tools for microarray data analysis. If you use R-GUI, you need to get the limma package from Bioconductor(http://www.bioconductor.org/). It's very easy to install bioconductor packages. Generally,If you have installed limma package,you can find a file named "usersguide.pdf" which should be in the path "C:\Program Files\R\R-xx\library\limma\doc". You can get the usersguide.pdf and Reference Manual.pdf from Bioconductor webpage.
http://www.bioconductor.org/
PLUS: You can also get the usersguide.pdf and Reference Manual.pdf from Bioconductor webpage through searching "limma" in the search textbox on the top right corner of the webpage.
I think usersguide.pdf is helpful to your study,there are many examples in it. Reading data, Pre-processing data, Statistics for differential expression, Case study...and so on...
After you running ever step following the help file, you may need to adjust the pvalue using p.adjust() function. Using the following commands to learn about the function, and to follow the help files.
>?p.adjust
>help.start()
actually, I would recommend CyberT instead of limma for differential expression discovery.
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