i would like to use the function treat implemented in limma, in order to test simultaneously the test significance of my microarray linear model fit and my design. Because i have never used in the past, the argument fit in treat refers to the output of lmFit or from the ebayes fuction ? Moreover, if i would like to put an absolut log fold change > 1 i use lfc=1 ?
And finally, i can use the function topTreat to get the output from treat ? Please excuse me for my "naive" questions but im a beginner in R.