Trouble with spillover matrix calculation r-script

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Computational image analysis of multiplexed Imaging Mass Cytometry acquisitions
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asasama12
Posts: 2
Joined: Fri Oct 04, 2019 6:28 pm

Trouble with spillover matrix calculation r-script

Post by asasama12 » Tue Oct 13, 2020 8:53 pm

Hello IMC experts,
My group has created and imaged a slide with individual antibodies dotted in a grid in order to calculate IMC metal spillover as described in Chevrier et. al., 2018, using the R-script posted on github (https://github.com/BodenmillerGroup/cyT ... t_long.Rmd) but have had issues running it all the way through.

I reach line 126 successfully, but when calculating the CATALYST based compensation, I get the following error:

Code: Select all

Error in CATALYST::assignPrelim(x = ff, y = ss_ms) : unused argument (y = ss_ms)
4.
re_from_dat(x, ss_ms = x[!is.na(mass), unique(mass)], minevents = 40, correct_bc = T)
3.
FUN(X[[i]], ...)
2.
lapply(dats_agg, function(x) re_from_dat(x, ss_ms = x[!is.na(mass), unique(mass)], minevents = 40, correct_bc = T))
1.
lapply(dats_agg, function(x) re_from_dat(x, ss_ms = x[!is.na(mass), unique(mass)], minevents = 40, correct_bc = T))
Has anyone experienced a similar problem, or have ideas for correcting?

thanks!
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votti
Posts: 26
Joined: Mon Nov 27, 2017 12:46 pm

Re: Trouble with spillover matrix calculation r-script

Post by votti » Tue Oct 20, 2020 3:53 pm

Hi,

Just as a cross reference, this question has been addressed/discussed on the Github repository:
https://github.com/BodenmillerGroup/cyT ... n/issues/1

I hope that the Repository with the improved description will be the default soon.

Please let me know on Github if something else doesnt work.

Best, Vito
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