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markrobinsonuzh / cytofWorkflow

MIT License
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Data preparation #32

Closed synatkeamsk closed 11 months ago

synatkeamsk commented 11 months ago

Dear respected professors,

Hope you are well. Thanks for building CYTOF package. I am a new users of CYTOF and I have flow cytometry data for analysis with CYTOF. I went through your tutorials (https://www.bioconductor.org/packages/release/workflows/vignettes/cytofWorkflow/inst/doc/cytofWorkflow.html#data-preprocessing) and run all your provided scripts. All works. However, once it comes to all my data, I am not sure how to prepare it for CYTOF because you did not provide it in your workflow.

In CYTOF workflow, I can use the following command to load the data, then I can run all your script. 

library(HDCytoData)
fs <- Bodenmiller_BCR_XL_flowSet()

I have fcs files for CYTOF, I am wondering whether you have instruction and tutorials how to prepare and load data into R so that I can replicate your scripts using my data. Sorry for the question as I am just starting to use it and find it very impressive. I hope you could help me. I am looking forward to your response.

Regards, Synat

markrobinsonuzh commented 11 months ago

Hi @synatkeamsk,

There are instructions in the text:

Alternatively, the files can be downloaded manually from the Citrus Cytobank repository and loaded into R as a flowSet using read.flowSet() from the flowCore package [29]. Importantly, read.flowSet() and the underlying read.FCS() functions, by default, may transform the marker intensities and remove cells with extreme positive values. This behavior can be controlled with arguments transformation and truncate_max_range, respectively.

Did you try that?

Best wishes, Mark