I’m sorry for the delay in my response and I thank you again for all the new info, which I am still trying to put in order. I tried to calculate the fold change according to your instructions (contained in your very first reply) and by opening the example of differential search that you suggested but still, I didn’t manage to obtain the exact fold change values reported in the table next to the heatmap, as well as in the downloaded probes–.csv file. I did manage to extract similar values or close to the ones expected, but they were clearly different although i did download the data, after having changed the color map setting of the heatmap, and by doing so, in other words, the scale of my results from the default z-score values to the log2 intensity ones. I made sure to apply the formula suggested by you (considering that my .csv values values at that point were all expressed in log2 intensity), meaning: fc = average log2(intensity)of all samples (with the heatmap resolution set to “Samples”) in the Target Structure minus the average log2(intensity) of all samples in the Contrast Structure. Any idea what may have gone wrong? Thank you again in advance
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