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YosefLab / ImpulseDE2

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Case-control heatmaps #16

Open mikefors08 opened 4 years ago

mikefors08 commented 4 years ago

Hello,

I am new to programming and I'm having difficulty understanding the heatmap output data. It is my understanding that ImpulseDE2 outputs heatmaps illustrating gene expression trajectories in either Case or Control groups. This explains how a gene is changing over time in either Case or Control samples. However, I would like to generate a heatmap illustrating the difference in gene expression over time (Case - Control). Is there a way (if it isn't implemented already) to generate heatmaps that contain the difference in gene expression for case compared to control at each time point?

This question originated when I was asked about the values used to generate the z-scores for transiently expressed genes. Are these z-scores generated from the gene expression values within that group (Case or Control) or are the z-scores reflecting the difference in gene expression (case-control) for each time point and plotted across time?

Thanks in advance as I know this is a relatively naive question!

MF

Balays commented 3 years ago

Hello MF, If you haven't found your answer yet, th z-scores are calculeted for the case and control independently. If you would like to visualize the difference between the two, you can carry out a pairwise comparison with DESEq2 and use the log2foldchange values as I think this is not implemented in ImpulseDE2.