I have normalized data from 60 arays(each array contains 26000 genes). I have done fold change and ANOVA2 analysis in R manually. Now I am left with file containing gene ids, ANOVA P values and respective fold change values (log2 ratios). Will it be possible to load this file to MeV and do clustering based on fold change values (log2 ratios) ?
Sure you can. Just create a *tab* delimited file with gene ids and log2 values in Excel or something you are familiar with.
If the gene ids are not unique it might be useful to add a column at the beginning of the as numeric index (1,2,3 ..n) just as a unique id for each row. The format would like :
UID tab GENE_ID tab SAMPLE_1 tab SAMPLE_2 tab …….SAMPLE_n
In MeV select the default loader (Tab delimited multiple sample files). Remember to UN-Check the Load Annotation box.
Just remember that since there won't be any annotation some of the modules will not work with your data. But clustering modules should be fine.