May be its very basic question for you all. I would like to perform 2 way ANOVA test for my NGS time series counts data. It is raw data counts by HT-Seq. I have 2 condition and for each corresponding diff. time points and their counts. Suggestion is to perform 2 way anova test. but problem is, i don't know the better way to prepare file for that in order to use R function like aov(). Help me to do so....
My raw counts (without normalization) like..
gene_name counts_value (for each condition and corresponding time points (36 sample in total) )
gene_1 2349 gene_2 3462380 gene_3 0 gene_4 123
- How to prepare (format of input) input file in order to use R functions
- is there any package (bioconductor or R) to perform this analysis
- may i have to normalize this raw counts before performing 2 way ANOVA