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compCytof

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SaraAli

Participant

Posts: 10

Joined: Wed Jan 10, 2018 3:37 pm

Post Thu Jul 12, 2018 3:36 pm

compCytof

Hi,

I'm trying to use CATALYST to compensate some data I have. I'm able to generate a compensation matrix but when trying to apply that using the nnls method I get the message "unused argument (method'="nnls")".
The same thing happens when I try to apply that to the dataset mp_cells.

I would dearly appreciate any advice as I'm an R novice!

Many thanks.
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markrobinsonca

Participant

Posts: 11

Joined: Wed Apr 19, 2017 7:35 pm

Post Thu Jul 12, 2018 4:28 pm

Re: compCytof

Dear Sara,

(this might go better in the 'CyTOF data analysis' board ..)

My guess is that you have an old version. Can you check that you are running R 3.5.x and using the latest release of the CATALYST package [1], which is currently 1.4.2? To check, you can run:

library(CATALYST)
sessionInfo()

Assuming you have some Bioconductor packages already installed, you can run:

BiocInstaller::biocLite("CATALYST")

.. to get the latest version (or more precisely, latest for the given version of R). If that doesn't work, let me know.

Best, Mark

[1] http://bioconductor.org/packages/releas ... ALYST.html
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SaraAli

Participant

Posts: 10

Joined: Wed Jan 10, 2018 3:37 pm

Post Fri Jul 13, 2018 1:25 am

Re: compCytof

yes, I had the older version, and it's working now after I've updated it.
Thanks a million! :)

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