Question

Cytofkit - Trouble with writing files after performing the analysis

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cjackson13 • 0

@cjackson13-11786

Last seen 8.1 years ago

Colorado

I am working on analyzing cytof data for my lab and while I have successfully been able to use the gui method as well as the step by step command option, I am having an issue with saving files once I have completed the analysis.

I need help accessing the csv files after performing an analysis using commands. I do not have trouble with the files being sent to the directory if using the gui option, however when I am using the command option of cytofkit, I cannot successfully save R.data or any csv files.

I am using the "cytof_writeResults" function and when it saves into the directory, there is only one csv file and it does not contain any information once I open it. Furthermore, the R.data file crashes the Shiny APP. I have set the "saveToFCS" value to false as I have already been able to save an FCS file and when I set it to true, I get this error:

Error in do.call(cbind, dimReducedData) : second argument must be a list

Is the cytof_writeResults function not working because I did not use the cytof function directly?

I like being able to use the commands so I can have more flexibility with my results so any help would be appreciated.

Thanks in advance,

cytofkit cytof write.csv output • 1.5k views

ADD COMMENT • link updated 8.1 years ago by chen_hao ▴ 30 • written 8.1 years ago by cjackson13 • 0

score 2 · Accepted Answer · 2016-11-03

Hi, Thanks for you feedback. Yes, cytof_writeResults function currently only works on objects returned from cytofkit main function. If reading the codes is not painful for you, you will find a way to save the results properly by looking into the cytofkit function. Best Regards, Chen Hao On 4 Nov 2016, at 4:08 AM, cjackson13 [bioc] <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> wrote: Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""/> User cjackson13<https: support.bioconductor.org="" u="" 11786=""/> wrote Question: Cytofkit - Trouble with writing files after performing the analysis <https: support.bioconductor.org="" p="" 89046=""/> : I am working on analyzing cytof data for my lab and while I have successfully been able to use the gui method as well as the step by step command option, I am having an issue with saving files once I have completed the analysis. I need help accessing the csv files after performing an analysis using commands. I do not have trouble with the files being sent to the directory if using the gui option, however when I am using the command option of cytofkit, I cannot successfully save R.data or any csv files. I am using the "cytof_writeResults" function and when it saves into the directory, there is only one csv file and it does not contain any information once I open it. Furthermore, the R.data file crashes the Shiny APP. I have set the "saveToFCS" value to false as I have already been able to save an FCS file and when I set it to true, I get this error: Error in do.call(cbind, dimReducedData) : second argument must be a list Is the cytof_writeResults function not working because I did not use the cytof function directly? I like being able to use the commands so I can have more flexibility with my results so any help would be appreciated. Thanks in advance, ________________________________ Post tags: cytofkit, cytof, write.csv, output You may reply via email or visit Cytofkit - Trouble with writing files after performing the analysis