Microarray software advice?

[Evelyn]

Hi all,

What software do you currently use for data analysis and what are the pros and cons associated with it? Is there a "perfect" system out there yet?

Thanks,

[mdfenko]

what type of data are you looking at (eg-cgh, gene expression,...)?

there is at least adequate software for each type of array analysis.

[Evelyn]

I'm just wondering if there is anything out there that handles gene expression, and SNP detection quickly and efficiently. I'm getting back into the field after being away for 6 years and I have a lot to catch up on... (btw, what is eg-cgh?)

[mdfenko]

eg is the abbreviation of exempli gratia, Latin for "for example"

cgh is the abbreviation for "comparative genomic hybridization"

we use genespring for gene expression (expensive and license must be renewed annually). we haven't been doing snps so i'm not sure what software will work for it.

one of our investigators is using a freeware package for ge but it is a pita to enter the data (the first time, at least). if you wish, i'll ask him what he has.

you can check out the software available at this website: http://www.tm4.org/

you can also check out the list of software on this webpage (scroll down a little): http://www.molecularstation.com/forum/microarrays-forum/1627-microarray-software-list.html
(note that this page is in the forum section of "molecular station", a very useful website)

[stylothecancer]

Hi,

At the moment GeneSpring GX ver 11 is able to analyze both Gene expression as well as genotyping data. =)

[Evelyn]

Thanks

@ mdfenko: I smiled upon reading pita. I'll have to use that more often.