User: ghogg

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ghogg0
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Posts by ghogg

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Comment: C: Re: Cydar. Can I Normalize CyTOF data with just one FCS file/batch and if so, wh
... Thank you so much for your response! Now that I think about it, a distribution normalization would definitely work best if you can assume a similar distribution between reference samples and trial samples, and I know the PBMC reference samples will have a significantly different intensity profile th ...
written 5 weeks ago by ghogg0
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Comment: C: Re: Cydar. Can I Normalize CyTOF data with just one FCS file/batch and if so, wh
... #first I load the non batch normalized files to check base level expression fcs_raw <- read.flowSet(path = "/Users/grahamhogg/Desktop/CyTOF Human T Cell FCS/relabeled_new", transformation = FALSE, truncate_max_range = FALSE, alter.names = TRUE) #Here I arcsinh normalize the data ...
written 7 weeks ago by ghogg0
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Comment: C: Re: Cydar. Can I Normalize CyTOF data with just one FCS file/batch and if so, wh
... Hi Aaron, Thank you very much for your advice. I have decided to use a subset of samples for which we have a PBMC control run on the same day, rather than risking normalization with only one sample/batch. I have also arcsin normalized the data prior to batch normalization. I have been using the qu ...
written 7 weeks ago by ghogg0
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Comment: C: Re: Cydar. Can I Normalize CyTOF data with just one FCS file/batch and if so, wh
... Thank you for your help! Best, GH ...
written 7 weeks ago by ghogg0
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Re: Cydar. Can I Normalize CyTOF data with just one FCS file/batch and if so, which normalization mode is recommended?
... Hello, I'm a novice R user, but have been tasked with normalizing some human CyTOF data, acquired over multiple days. I have been working with the Cydar package in the hopes of normalizing between different runs. The question I have is whether I can normalize batch effects if we have only one samp ...
normalization cytof cydar written 8 weeks ago by ghogg0 • updated 8 weeks ago by Aaron Lun25k

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