Question: FCSTransTransform() implementation in flowCore
0
gravatar for Nik Tuzov
28 days ago by
Nik Tuzov70
United States
Nik Tuzov70 wrote:

Hello:

It looks like the only difference (please correct me if I'm wrong) from FCSTrans implementation is that flowCore uses it's own C++ implementation of biexponential_transform() in place of original C implementation in FCSTrans.

1) If FCSTransTransform() was meant to reproduce FCSTrans, why wasn't the original biexponential_transform() used?

2) Is it possible to find the original C source? I looked on Sourceforge:

https://sourceforge.net/projects/immportflock/

but it's not found there.

Regards, Nik Tuzov

ADD COMMENTlink modified 28 days ago by Jake Wagner100 • written 28 days ago by Nik Tuzov70
1

Hi, 2) the original code of FCSTrans is R code and could be found at https://sourceforge.net/projects/immportflock/files/FCSTrans/ Regards

ADD REPLYlink written 28 days ago by SamGG190
Answer: FCSTransTransform() implementation in flowCore
3
gravatar for Jake Wagner
28 days ago by
Jake Wagner100
Jake Wagner100 wrote:

Well, this was a bit before my arrival on the team for flowCore, but I think most of the answers to your questions can be found in this commit:

https://github.com/RGLab/flowCore/commit/30d9fc3fd7e46f9b75a45c6410b4a9c43233a8d8

The original C implementation of biexponential_transform is there, along with its C++ replacement.

1) I believe Mike was just updating the legacy C code to hook it in to Rcpp::compileAttributes for auto-generating the R bindings. See other commits from right around that time: https://github.com/RGLab/flowCore/commit/a5aaaf39466699767b14ad25a6e93ede600cb540 https://github.com/RGLab/flowCore/commit/df4d7ef382b46761920a34fbda8a43e8aad939b4

2) Agreed, the sourceforge link (including yours SamGG), has the R source that calls biexponential_transform but not the C source for biexponential_transform. You can find that in the first commit listed.

Mike may have more insight, however.

Hope that helps, -Jake

ADD COMMENTlink modified 28 days ago • written 28 days ago by Jake Wagner100

Thanks for replying. Do you think the automatic width calculation inside FCSTransTransform() is helpful and often used?

ADD REPLYlink written 27 days ago by Nik Tuzov70

The estimateLogicle function usually does a good job. Look for it in HowTo-flowCore

ADD REPLYlink written 27 days ago by SamGG190
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