I contact you to understand how you calculate the relative fold change of MS data.
I would like to use the TPP package (bioconductor) which apply their workflow on IsobarQuant output. In their data, they have a table containing the relative fold change for each temperature. The goal is to formate our data (from MaxQuant) to apply this package on it.
I tried to understand your script working on it but I'm not sure to follow each step.
Usually, to calculate the relative fold change we apply a log2 transformation then a normalization. Do you do the same thing? Or just doing the ratio between raw intensities?
Dear IsobarQuant developers,
I contact you to understand how you calculate the relative fold change of MS data. I would like to use the TPP package (bioconductor) which apply their workflow on IsobarQuant output. In their data, they have a table containing the relative fold change for each temperature. The goal is to formate our data (from MaxQuant) to apply this package on it.
I tried to understand your script working on it but I'm not sure to follow each step.
Usually, to calculate the relative fold change we apply a log2 transformation then a normalization. Do you do the same thing? Or just doing the ratio between raw intensities?
Do you have a paper on this that I can read?
Thanks in advance for you return. Karen