I am dealing with different microarray analysis in R, and I have three questions. I took a look, and I haven't found an exact answer for any of them. If there is already one, sorry :(
-Concerning the package oligo: Is there any way I could create an annotation for a microarray using CLF, PGF files and etc.? I am working with Human Gene 2.0 ST arrays and I cannot install the XPS package due to certain library problems when installing ROOT (sigh). Is there any alternative? I need to be able to annotate each probe for ulterior analysis.
-I also have to analyze custom gene expression microarrays from Agilent, using R. Is there any special way to procede? I imagine that after the DE analysis, I will have to blast the sequences of the probes to my genome after analyzing it, but I would appreciate any advice or protocol. Is there any special library I should use for the DE analysis, being it a custom microarray from Agilent?
-Also, a (maybe) stupid question. When using makeContrasts from limma for three groups, one of them a control, it does not say which group differ in what, and you have to use pairwise comparisons after that. Then... what is the meaning of using the ANOVA for these three groups?
Thank you all for your help, and sorry for bothering you. Have a nice day!!