Preprocessing of input FCS files

[ashipde]

The FCS files of my CyTOF data have variables (columns) of different types

• for immune cell lineage markers like CD3 and CD19
• for cell state markers like Ki67 and pAkt
• for other variables like 'Time' and 'Event length'

I want to use SAUCIE for both batch correction and clustering. For clustering, I want to use only the cell lineage markers.

1. Should I preprocess the FCS files to remove any column that is not pertinent for clustering (such as for 'Time' and cell status markers)?
2. Should the data be processed in any other way, such as log2-transformation or arcsinh transformation? Raw data values in the files range from 0 to >15,000.

Thanks.

[mattamodio]

Hi, thanks for using SAUCIE! If you don't want to use certain columns, you can leave those column indexes out of the file cols_to_use.txt, and SAUCIE will ignore them. If you want to batch correct them but not cluster them, you can run it twice with different values in the cols_to_use.txt file. As for pre-processing, SAUCIE.py performs an asinh transformation as is typical for CyTOF data, so you don't need to do that ahead-of-time if you use SAUCIE.py.