Can Significant Analysis Of Microarray Be Done Via (Bio)Python, Besides R And Excel?

Question

[Olivier]

Hello everyone

Is Significant Analysis of Microarray only available on R and excel? I would like to know if there are any options available on python/ biopython or even free software for that purpose on a linux platform.
I don't have Excel and I still have to struggle with R basics.

Thanks

[Neilfws]

I'd recommend that you persist with R. Yes, it is a steep learning curve, but it offers so much potential that ignoring it is unwise.

[Olivier]

You are very right indeed.. I think it was the fear of mixing python and R syntax that made me shy away from persisting with R, because I feel more at ease with python and its nice modular methods. But I'm starting to realise that R might have a slight edge when it comes the length/ readability of code when working with numeric data. Things tend to get longer with numpy, at least for me. Thanks a lot.
I've tried SAM with both R (siggenes) and Tm4(MeV) and got it working (yay!). I've just got to interpret/ fine-tune now.

Answer 1

[venks]

You can find something useful in http://www.tm4.org/

This is a suite for microarray analysis

Good luck

[Neilfws]

Specifically, http://www.tm4.org/mev_manual/sam.html.

Answer 2

[Charles Warden]

There is also limmaGUI, which provides a user interface for analsyis:

http://www.bioconductor.org/packages/2.14/bioc/html/limmaGUI.html

I would prefer limma to SAM anyways, so I would recommend trying this

[Olivier]

Thanks. Got to put that on my to-do list.