#2 Question about Peca output files

[Amanda Guise]

Hello again,
I have a couple questions about the Peca output files:

1. Are the reported Rate Ratios and CPS vlaues in the data_R_CPS.txt file only for protein level regulation for the combined RNA/protein dataset?

2. Is there a way to extract rate ratio and change point probabilities separately for the RNA and protein level? In my output file from the Peca analysis (data_R_CPS.txt) I see Rate Ratios that match the values for Synthesis from the gene_protein.pdf output (and degradation plotted appears to be 1-Synthesis).

3. Is there a place that I can look to find an explanation of the other output files (e.g., xRyD.pdf, trace_tau2.pdf)?

Any advice would be appreciated!
Thank you!
Amanda

[Hyungwon Choi]

Hi Amanda,

1. Each run performs only the "protein-level" analysis. If you want to run the RNA-level analysis, you have to create a data set where the actual RNA data is placed as protein data and a matrix filled with "1" is placed as RNA data. This is of course under the assumption that you have equal DNA copy number for each gene.

2. The values are "scaled" values of the ratio. There is a mathematical reason why these values cannot be estimated in the raw scale: there are infinitely many solutions of (synthesis, degradation) rates. We're developing a version that can do this for the case when you have pulsed SILAC at the moment, but for regular label-free data sets, this will take some time (may not be possible at all).

3. We will review the manual and probably create a tutorial for all this. Those are mostly model diagnostic plots to make sure your PECA model is sound. If you'd like to discuss, please post more questions.

Thank you for trying PECA.
Hyungwon

[Amanda Guise]

Thank you! This is very helpful information. I was able to run the RNA vs. "gene" version with your advice. I have been running PECA so far with only one replicate, but plan to run it again once I have more data and it would be great to discuss the modeling diagnostics then. Again, thank you so much for your quick and detailed reply (and for developing PECA!).
-Amanda