I am trying to reproduce a methodology described to identify changes in gene translation ratios using microarray experiments described in PubMed ID19804760, page 158. To calculate translational ratios, one divides the translation ratios from the experimental group by the translation ratio for the control group. My issue is that the translation ratio (Rn) in each group (control or experimental) comes from a microarray experiment that divides expression levels in ribosomal polysomes by the expression in ribosomal monosomes. Therefore each Rn (R1, R2, etc) has its own statistical significance. So for R1 it is p1 and R2 it is p2 (ANOVA analysis). How do we calculate the statistics of the ratio between R1 and R2 for example?
'Dividing an expression ratio by another' can be treated as a log-scale difference if with transformation. Once the GSE16738 data are log-transformed and normalized, it should be straightforward to conduct the analysis by using the 'limma' package with a 2-factor-2 level (3 repeats) design matrix.
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