Actually I know that they set the algorithm in a way that
Only proteins with fold changes bigger than [fcCutoff * (1 - fcTolerance)
or smaller than 1/(fcCutoff * (1 - fcTolerance))]
will be used for curve fitting. Additionally, the proteins fulfilling the fcCutoff criterion without tolerance will be marked in the output column meets_FC_requirement
.
I tried to set the fcCutoff = 1,fcTolerance = 0
because I thought 1*1 =1 for bigger situation and 1/1 will be 1 so I will set them somehow to a number that I will be able to plot the curve for all proteins.
and I got the following error
Fitting 3663 individual dose response curves to 3663 proteins. Error in fitDRCurve(protID = unique(fcSplit[[i]]$id), expName = unique(fcSplit[[i]]$experiment), : task 557 failed - "missing value where TRUE/FALSE needed"
I want to obtain the curve fitting for all proteins and not only those that met the above criteria , how can I do it?
I also would like to know the fcCutoff and fcTolerance they use or how to select a optimal one.
What I take their data example and use analyzeTPPCCR which automatically do all the steps.
Many thanks in advance again
@dorothee.childs this is totally true. what I need to know is how to have the pEC50 for all proteins ? instead just putting a threshold and making it as stabilised and destabilised, I also need to have the values for unaffected. By the way, can you please give the script that you plotted the figure in box 3 of Franken et al. (2015). Nature Protocols, 10(10), 1567–1593 ? it is totally impossible for me to reproduce the same plot as you reported in that protocol