Standardising exported data with different channels
I’m been having a real headache trying to analyse samples which have had a few new channels added to the sample data upon acquisition. This has resulted in basically two panels which need to be analysed side by side.
I have very basic understanding of R, the analysis I’ve been trying to perform has been on CyTOFkit.
I’ve attempted several different ways of standardising the fcs files, transforming into excel, deleting extra channels, and standardising channel names, then saving as FCS with no luck. I’ve tried using Premessa R program which was recommended here, this was useful as I was able to remove extra channels but for some reason channel names changed between different sample acquisition, and even using Premessa and changing channel names I’m still not getting a unified panel to allow me to analyse all of my samples.
I’ve attached an image to show the problem, even after removing discrepant channels and changing the names of the channels to match the samples are still not standardised!
Any help would be much appreciated!
Thank you.
Before Premessa
https://tinyurl.com/ycffreug
After Premessa
https://tinyurl.com/ycd9arqx