Hi Tom,

Thank you very much for yoru reply!

When I export FCS files from Cytobank they are without arsinc transformation.

SO yes, step for arsinc transformation would be necessary.

I am looking forward for the script!

My mail is

julia.majewska@weizmann.a.cilAgain, thank you a lot!

For the second part of the question:

For data analysis step, we are pooling all PBS samples together (for example 6 mice PBS treated) and we are also pooling all treated mice (at the end of pooling we have 2 samples, 1st - PBS, 2nd treatment).

The cells of interest are rare events, therefore the aim of pooling is to increase event size and significance of analysis.

If we would analyse each sample separately, then we would see if particular sample behaves as an outlier, as a dot on a graph.. However, we dont see it as we work on pooled samples.

The question is how show that distribution of expression for different markers is compabarable within treatment, therefore pooling can be done.

We have done it by violin plots, showing expression for each marker for all mice (treated vs untreated). I was wondering if there is any other way.. (i think tSNE is not the most readable).