hello.. I have miRNA hybridized CEL files for control and experiment. now i want to find out differential miRNA and also want to identify that how many miRNAs are hybridized. I do not know which package and method was used for miRNA analysis. I did Microarray analysis of RNA cel files and for that i used affylmGUI package and RMA method. but for the differential miRNA analysis same package can we used? If yes then i did the analysis and i got 20707 miRNAs with M and P values. Now i did not get that how many miRNAs are hybridized. I am so confused so Can any one help me in the field of micro array analysis? [[alternative HTML version deleted]]

hello... Can anyone clear one more thing about the miRNA analysis. As I mention earlier I have two miRNA cel files(rice) for one is control and other one is experiment . when I did analysis for differential miRNA using affylmgUI package. I got total 20707 mirna with significant and non significant P value. In this analysis, how can we identify that out of 20707 miRNA, which miRNA is hybridize properly. thanks regards deepika ---------- Forwarded message ---------- From: deepika lakhwani <lakhwanideepika@gmail.com> Date: Tue, Oct 1, 2013 at 10:12 AM Subject: Regarding miRNA analysis To: bioconductor@r-project.org hello.. I have miRNA hybridized CEL files for control and experiment. now i want to find out differential miRNA and also want to identify that how many miRNAs are hybridized. I do not know which package and method was used for miRNA analysis. I did Microarray analysis of RNA cel files and for that i used affylmGUI package and RMA method. but for the differential miRNA analysis same package can we used? If yes then i did the analysis and i got 20707 miRNAs with M and P values. Now i did not get that how many miRNAs are hybridized. I am so confused so Can any one help me in the field of micro array analysis? [[alternative HTML version deleted]]