frelinger review

[stefanv]

@jfrelinger

Nice paper, thanks! Since I am not a domain expert, just a few editorial comments:

• "few opensource tool" -> tools
• Introduction contains quite a bit of jargon ("monoclonal antibodies are conjugated"): if possible, but some equivalent "English" in brackets that others may understand
• What is on the x axis of the EQAPOL histogram?
• Gallery is missing at provided url
• caner -> cancer

[stefanv]

/cc @ahmadia

[ahmadia]

@jfrelinger

These are comments from Eric Jabart:

I'm far from an expert in programming, so it's difficult for me to comment on the specifics of the programming aspects.

However, as an open-source tool which would recapitulate what a lot of proprietary software does out there (which is quite expensive) it sounds great.

Although it's 2 years old, I think the references are still a bit old, and some of them could be refreshed.

Here are a few of my comments below.

---

A grammar/spell check should be done - there's a least 1 typo in the abstract.

A few more references should be added - e.g when talking about 12-color instruments and such; there are new systems out there too (since 2012) that may have new modalities - perhaps a brief mention of these.

Would be nice to give examples of the cost of these proprietary software packages in comparison - to show how useful this open source software is.

The first figure is a bit confusing -and could be even more generic - no need to bring in specific cell types and surface markers - but is the 'helper T-cell marker' supposed to be an fluorochrome-labeled antibody? I think it should just be made a little clearer to reflect the text. I do see that CD8 and CD4 are used again later - so maybe a little more description of them is necessary in the first figure caption (ie using surface markers CD4/CD8 detected with fluorochrome-labeled antibody - which is called the "helper T-cell marker" in the figure)

"Much work is needed to train expert operators to standardize gate placement and minimize variance" - spell/grammar check

et al. - same

Overall I think this is a very useful software package and likely to be well-appreciated, especially given the cost of current software packages. There are not many open-source flow cytometry analysis tools out there so it has a high probability of being adopted if it works well.

[jfrelinger]

• "few opensource tool" -> tools

This has been fixed

• Introduction contains quite a bit of jargon ("monoclonal antibodies are conjugated"): if possible, but some equivalent "English" in brackets that others may understand

Additional language to describe the technical terms in more 'plain English' have been added.

• What is on the x axis of the EQAPOL histogram?

The missing X label has been added and the figure mentioned in the figure caption

• Gallery is missing at provided url

This has been fixed.

• caner -> cancer

This has been fixed.

• A few more references should be added - e.g when talking about 12-color instruments and such; there are new systems out there too (since 2012) that may have new modalities - perhaps a brief mention of these.

Additional references on the expanded capabilities of current flow cytometry techniques have been added.

• Would be nice to give examples of the cost of these proprietary software packages in comparison - to show how useful this open source software is.

Commercial software packages for flow cytometry focus primarily on gating based analysis. They also provide graphical user interfaces to ease examining data and determining gate placement. Tools for model based analysis are rudimentary and rare. While fcm provides objects and methods to perform traditional gating based analysis, it is not a traditional graphical gating based user application. It would be a good library to build such an application. Therefor we do not feel such a comparison is as valuable.

• The first figure is a bit confusing -and could be even more generic - no need to bring in specific cell types and surface markers - but is the 'helper T-cell marker' supposed to be an fluorochrome-labeled antibody? I think it should just be made a little clearer to reflect the text. I do see that CD8 and CD4 are used again later - so maybe a little more description of them is necessary in the first figure caption (i.e. using surface markers CD4/CD8 detected with fluorochrome-labeled antibody - which is called the "helper T-cell marker" in the figure)

The caption on figure one has been expanded on. It now describes the process of labeling cells, laser excitation and recording of the fluorescent emission.

• "Much work is needed to train expert operators to standardize gate placement and minimize variance" - spell/grammar check

This has been fixed

• et al. - same

This has been fixed.