diffrential expression analysis

Question

[au.rinki.bio]

Hello biostars, i am working on microarray data analysis and trying to find out differentially expressed genes for this i am using limma package. becoz i am new in this field i face problem with limma. i have downloaded microarray data( cel files) related to my interest it consist total 24 sample,12 for normal 12 for disease. i am working on windows based system. i have installed limma package. how to proceed futher i am unable to do. i am following limma user guide() instruction but still face problem. plz suggest me any tutorial related microarray data analysis(cel files) using limma package.

[au.rinki.bio]

how to prepare taget file from these cel file which input file for limma?

[andrew.j.skelton73]

It's in the Limma Users Guide (Hint: look at page 101). Try to be more specific with your questions, generally asking for tutorials and commands to blindly run isn't the best way to learn how or why you're doing something.

[au.rinki.bio]

page no. 101 you have specified. this is for single channel microarray data analysis. i have affymatrix microarray data (GSE14407) data have normal vs cancer sample on same microarray chip.

Answer 1

[apeltzer]

If you are running things on Windows and are unable to figure out how to use limma by googling etc, maybe you're better off by trying a different tool for interactive analysis of microarray data. No offense, but using a specialized R package for any kind of analysis is probably very hard if you don't have experience (which I'm guessing from your post) ;-)

I didn't test it myself, but maybe you could have a look at Mayday http://it.inf.uni-tuebingen.de/?page_id=248 . That should be much easier for you and is absolutely feasible for your kind of analysis.