I am performing some research involving microRNA-mRNA integrated analysis and I would like to use the MMIA tool. To use this tool I have to prepare two properly formatted files: one with microRNA data, and second with mRNA data. On the MMIA website (http://epigenomics.snu.ac.kr/MMIA/documentation.html#output) there is a very wide description of requirements for files, and some other available options. They say that my microRNA file should be tab - delimited, and looks like as follows:
|hsa-let-7a||expression value ...||...||...||...|
Also, they say, that the file containing microRNA data has to be prepared to have up-regulated microRNAs in group 2 in comparison with group 1.
And here is my question: how to and using which tool performe such a differential expression analysis to have ONLY upregulated microRNAs in group 2, not group 1 or mixed.
Such a file I am preparing in the following way:
1. I download my GSE files from GEO for microRNA and mRNA using R and GEOquery.
x<-getGEO('GSExxx)[] write.table(data.frame(fData(x),exprs(x)), sep="\t", row.names=FALSE, file="xxx.txt"
It generates file containing all microRNA identifiers from matrix in a rows and all samples in a columns.
2. I process this file using Babelomics 4.3 tool to get rid of replicates, and missing values.
3. Then, I manually change the names of samples and categorize it into two analyzed classes (f.e. c1 and c2).
4. MISSING THING: categorizing my microRNA data to have only up-regulated in group 2.
So, what eventually am I doing wrong, or how to change it? I am a bit fresh in bioinformatics, especially in that kind of analysis, so please, help me.
Thanks in advance!