Values below zero

[tomashhurst]

Hi there,

I'm using the code from CytofBatchAdjust and a number of other batch alignment tools in our Spectre package. We use this for the analysis of a variety of cytometry data, including flow. One feature of CytofBatchAdjust that I have noticed is the values below zero are clipped at zero (see attached image, Y axis = pre-aligned, X axis = post-aligned to 95th percentile), presumably because this code is intended for use with CyTOF data (where all the values are zero or above). In our workflow I have some workaround options, such as rescaling the data in each channel between 0 and 1, but it might be advantageous to allow for the code to handle negative values, so that it could be used direct with flow data as well.

[SamGG]

Hi Thomas,
I am going to rework on CBA those days. I want to add an Excel file as the file input in order to simplify things. I don't know if you did that already. I will look into the zero question.
Best.

[jsim91]

Some time has passed since this issue was opened so perhaps Thomas has already solved the problem. If not, a few lines are driving the truncation of values at zero. This is obviously a problem when using the function for flow data. Lines 615-618 of the BachAdjust.R script force negative values post-correction to 0. Commenting out these lines and re-sourcing the script solves the issue. Here are two plots. The first shows the truncation problem along the y-axis values. The second shows the distribution after commenting out lines 615-618


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Perhaps an argument could be added to the function that allows the user to specify if the source is flow or cytof.