Figure 5
Validating the microarray normalisation procedure with Q-PCR.
6 H3Ac (top) and 5 Gcn5p (bottom) sites were examined with Q-PCR. For each normalisation stage (Stage 1 — Stage 4) a comparison between the microarray and Q-PCR data was made. Additionally all datasets were quantile normalised as one (Quantile Normalised). For each analysis Q-PCR data values were scaled to the microarray data values. Arrows represent 2 data points, from 2 experimental conditions, with the head of the arrow marking the second condition. The Gcn5p data shows arrows for untreated to time point 1 (t1; black) and time point 1 to time point 2 (t2; red). The angle of the arrows relative to the line y = x shows the similarity of the change between experimental conditions recorded by the two technologies, with angles close to this angle representing similar changes in both technologies. The distance of the points from the line y = x represents the similarity of values between the two technologies, with points closer to the line having more similar values. Bar charts show Q-PCR (shaded) and microarray (unshaded) values in preprocessed (Stage 1) and fully normalised (Stage 4) datasets for untreated (white) and treated (black, H3Ac; grey and black, Gcn5p) datasets. Error bars show standard errors.
