Added MIQE guideline comparison table

ropensci / tidyqpcr

quantitative PCR analysis in the tidyverse

https://docs.ropensci.org/tidyqpcr/

Other

51 stars 18 forks source link

Added MIQE guideline comparison table #148

Closed DimmestP closed 2 years ago

DimmestP commented 2 years ago

Adds draft table in README below software features to compare tidyqpcr to other current software according to compliance with MIQE guidelines.

Current tidyqcr is compared to pcr, HTqPCR and NormqPCR. I have not yet finished comparison with qpcR as the documentation is a little convoluted and I need more time to find out exactly what is being done.

There remains a few question marks in the tidyqpcr column as I am not entirely sure if we fully complete the requirements by MIQE on those topics.

ewallace commented 2 years ago

Thanks Sam, a couple of comments here

Conceptual Considerations - I don't know if all those headings are relevant. E.G. Limit of detection isn't something we formally test in tidyqpcr.
Method of Cq determination is I think asking about how Cq is determined from the amplification curve. For tidyqpcr we could say "external" as so far we are taking that from instrument software.

What can I do here? Will you do a next draft or do you need me to?

DimmestP commented 2 years ago

@ewallace if you have time could you go through the MIQE guildelines and help fill out if tidyqpcr fulfils them. There are a few that I have put a question mark in. I am not sure if we need to address them. I have just copied the titles straight from the table in the MIQE paper so I think we need to add a sentence or too to explain why tidyqpcr does not address them (or does not need to address them).

I am currently working through the qpcR package entries.

ewallace commented 2 years ago

I've tried to address most of these, with nuance and explanations.

@DimmestP Please can you check & fix the "Method of Cq determination" line? tidyqpcr does not do this at all because we don't have a Cq calculation capability, that is issue #19. By contrast, qpcR has Cq calculation as a core capability, that is what it means by "sigmoidal model selection". I don't know about the other packages.

I left a FIXME on that line to make sure we, well, fixed it.