Hi @guoshou @mzhangyb
I am currently using the PecaR to estimate protein synthesis rate and degradation rate from my label-free proteomics data. I had been successfully employed the pipeline and had some results after a few iteration. However, I am struggling to interpret the insights yielded from the mRNAprot.pdf file since in the tutorial there is no example on that. I would summarise my issues here:
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Interpreting the scatter plots. I would assume that the y-axis represent the value of either mRNA or protein abundance value but not sure what does the x-axis mean? It seems very crowded and when I manually checked the file the peca_R.py used, I saw numeric values and there are 100 of them. Could you kindly suggest what are they and how to interpret them?
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As you can see, the top value in the y-axis is mostly 1, some other case has very large number (300,300,etc). Does the pipeline apply any scaling step into the data? Also I assume that the value I saw in the y-axis of either the synthesis or degradation is the value of ks and kd but please correct me if I am wrong. If I want to convert them into % of synthesised or decay protein over day. How should I do that?
Thanks for reading my long questions and hope to hear from you soon.
Q
Hi @guoshou @mzhangyb
I am currently using the PecaR to estimate protein synthesis rate and degradation rate from my label-free proteomics data. I had been successfully employed the pipeline and had some results after a few iteration. However, I am struggling to interpret the insights yielded from the mRNAprot.pdf file since in the tutorial there is no example on that. I would summarise my issues here:
Interpreting the scatter plots. I would assume that the y-axis represent the value of either mRNA or protein abundance value but not sure what does the x-axis mean? It seems very crowded and when I manually checked the file the peca_R.py used, I saw numeric values and there are 100 of them. Could you kindly suggest what are they and how to interpret them?
As you can see, the top value in the y-axis is mostly 1, some other case has very large number (300,300,etc). Does the pipeline apply any scaling step into the data? Also I assume that the value I saw in the y-axis of either the synthesis or degradation is the value of ks and kd but please correct me if I am wrong. If I want to convert them into % of synthesised or decay protein over day. How should I do that?
Thanks for reading my long questions and hope to hear from you soon.
Q