I am new to R and want to analyze miRNA data set of 3 groups. I am able to normalize, designing matrix and contrast matrix and differential expression. But what I am facing is affy chip has lot of other miRNA probes which I guess I am not able to filter them out. I just want to select human miRNAs from chip and do analysis and compare the three groups. Can any one help me in this
If I understood correctly, you want to filter them out-> just the human miRNAs. You can use grep for that Here is an example (loads a fasta file containing the hairpins annotated in miRBase and filters the human ones)
library("Biostrings") aux <- read.RNAStringSet("hairpin.fa") names(aux) grep("hsa",names(aux)) aux[grep("hsa",names(aux))]
You can adapt it for your task. Hope this helps.
I just want to study differential expression of human miRNAs and compare 3 gruops. I have used affy chips (mirna20). Just 2 weeks before I started learning R. Dont know much. During these days I learned how to load, read, normalize(RMA) data. I will appreciate if some one will help me out or direct me towards relevant example. Thanks in advance