Does setting transformation=F in read.flowSet and read.FCS remove the transformation already done by FlowJo?

[denvercal1234GitHub]

Hi there,

Thank you for the package.

I had FCS files that I obtained by converting the channel values exported from FlowJo (which meant they had already been transformed in FlowJo and will not need further transformation) into FCS files using Spectre::write.files() function as mentioned in issue #243. So, these FCS files should already been transformed.

Would you mind confirming that by running flowCore::read.flowSet(path=fcs.dir1, pattern="*.fcs", transformation = FALSE, truncate_max_range = FALSE) setting transformation=F will not remove the transformation of the input FCS files because it only meant that flowCore will not perform additional transformation to the input FCS, and this read.flowSet function therefore will only convert the FCS files into a flowSet object?

Thank you for your help.

[SamGG]

Hi,
When transformation = TRUE, read.FCS applies a linear transform; it does not remove any previous, it applies a new one on the data as they are. When transformation = TRUE, no transformation is applied.
I don't know what it is exactly done in your FlowJo/Spectre pipeline. If you export FCS from FlowJo as FCS 2.0, I am quite confident about getting transformed intensities/channels. Apart from FCS 2.0, I would not bet a penny without having tested.
Best

[mikejiang]

This transformation refers to something different from the one performed in flowjo, it has to do with PnE/PnG keywords, I don't think you need to concern about this parameter, it has no interferes or impact to your data, as @SamGG pointed out