Entering edit mode
6.4 years ago
Joe Kherery
▴
120
Hello .. Good evening.
I have worked with microarray and trying to reproduce some works with R however the works usually use commercial softwares as Partek software or agilent technologies software.
What you think, the difference in results is very great when R and commercial softwares?
PS. Often they use ANOVA, have any way to use that test using LIMMA?
Respectfully yours
Kherery
If i clearly understand your question you want to use the LIMMA package to perform ANOVA in your microarray analysis?
Yes if there is a way to do this using LIMMA and if there is a very big difference between analyzing in commercial softwares vs R?
There should not be any difference if they use the same methods and filtering criteria.
What can happen, though, is that commercial tools will assume that the user has minimal knowledge of the algorithms and will therefore do a lot of filtering on behalf of the user. They are generally tailoured for people coming from a wet laboratory background. The functions in R do the same, but there is more flexibility in R, and all code is open source.
What I find also happens is that algorithm versions and annotations in commercial tools become outdated very quickly, whereas in open source environments these can be updated more quickly.
For me there is no comparison and I would favour the use of R for microarray analyses. However, I have years of experience under my belt of analysing various types of microarrays.