I am sorry to disturb you! But I really need your help for the usage of sigPathwy.
Actually, I want a sliding window analysis for possible chromosome expression pattern mining. My research microorganism is a plant pathogen, Gibberella zeae, and I first used SAS to divide locus number with 10, 20, 30, or 40 on the fungal chromosome according to their location. I really want to see whether among the continual 10, 20, 30, or 40 locus has some expression pattern that different from rest genes. Because I know sigPathway (R package, pathway analysis with microarray data) can do this kind of job. What I use SAS to do is to subset locus in arbitrary genes numbers, such as 10, 20, 30, 40, or so on, and I hope to use sigPathway to analysis whether these genes chromosome location have effect on its gene expression.
When I used sigpathway to analyze my microarray data, it made my computer out of memory. I have tried the following R codes in several computer, but it always the same, even if it computed more than one day, it can not get any results. I also try to use memory.limit(size=NA), it dosen't work too.My computer is a cor duo 2G DDR2, I think it is large enough for my job. Would you please point out my problem and give me some suggestions? Thank you very much.
I attach my microarray data and R codes in the attachment, and I hope you can have a look.
#the following code is for annotation list initiation.