flowCore biexponential transformation

Question

[Biomed-jeh]

Hello Biostars,

I'm currently working with flow cytometry data and have successfully loaded my .fcs files into my R session. I've also generated panel data with marker classes (state or type markers). At this stage, I'm looking to transform my data using different methods, such as arcsinh, biexponential, and logicle.

Here's an overview of my current progress and the specific issue I'm facing:

1. Data Loading:

   • My flowSet object is named 'fcs_data.'
   • I have another object, 'markerstotransform,' which contains the FCS column names that need transformation.

2. Arcsinh Transformation:

   • I have successfully applied arcsinh transformation using the following code:

     cofactors <- estParamFlowVS(fcs_data, channels = markerstotransform)
     fcs_transform <- transFlowVS(fs = fcs_data, channels = markerstotransform, cofactors = cofactors)
     

   • I can visualize the arcsinh-transformed data using a density plot.

3. Issue with Other Transformation Methods:

   • I'm interested in trying other transformation methods like biexponential and logicle.
   • However, I've encountered challenges and am seeking guidance on how to implement these methods effectively.

I would greatly appreciate any guidance or assistance from the community to help me address this issue. Thank you in advance for your support.

[jv]

However, I've encountered challenge

We can't help you if you don't describe what the challenges are that you are encountering. Do you get an error message when running your code? If so, please provide your code and the error.