Issue with dimesnionality reduction/data analysis

[jenkinmt]

Hey all,
I'm trying to use the shiny app to analyze some de-barcoded data on live singlet FCS files. I am able to pull up the shiny app, upload the files, and select the parameters for analysis. However, when its finished I get this really long error message:
Warning in readFCSdata(con, offsets, txt, transformation, which.lines, scale, :
Some data values of 'tsne_1_linear' channel exceed its $PnR value 74 and will be truncated!
To avoid truncation, either fix $PnR before generating FCS or set 'truncate_max_range = FALSE'
Warning in readFCSdata(con, offsets, txt, transformation, which.lines, scale, :
Some data values of 'tsne_2_linear' channel exceed its $PnR value 70 and will be truncated!
To avoid truncation, either fix $PnR before generating FCS or set 'truncate_max_range = FALSE'
Warning in readFCSdata(con, offsets, txt, transformation, which.lines, scale, :
Some data values of 'Rphenograph_clusterIDs' channel exceed its $PnR value 15 and will be truncated!
To avoid truncation, either fix $PnR before generating FCS or set 'truncate_max_range = FALSE'
Writing results Done! Results are saved under path: /var/folders/3n/cx37cm9d6_725ym8brb2r2yw0000gn/T//Rtmpx8a9XH
/var/folders/3n/cx37cm9d6_725ym8brb2r2yw0000gn/T//Rtmpx8a9XH/f2b1ff4c261ed311ea989c17/0.zip

The data file it outputs is a text document with the letters "PK" in it. I am using a Mac OS and have taken the necessary steps to ensure cytofkit2 can run on a Mac. I tried setting 'truncate_max_range = FALSE' but that didn't solve the issue, either. I have tried analyzing with both UMAP and tSNE and get the same result each time. I was wondering if anyone else had run into this issue?

Thanks,
Matt Jenkins

[raman91]

Hi, thanks for the feedback. Could you please install again and check?

[jenkinmt]

okay will do. I forgot to mention that I am using RStudio version 4.1, and use the code below to install cytofkit2
if(!require(devtools)){
install.packages("devtools") # If not already installed
}
devtools::install_github("JinmiaoChenLab/cytofkit2",force=TRUE,depencencies=TRUE)

[jenkinmt]

I am still getting the same error as in my initial post

[jenkinmt]

Is there anything else I can try to get cytofkit2 to work?

[raman91]

Hi, can you check the output path if there is a zip file of cytofkit ? : /var/folders/3n/cx37cm9d6_725ym8brb2r2yw0000gn/T//Rtmpx8a9XH
/var/folders/3n/cx37cm9d6_725ym8brb2r2yw0000gn/T//Rtmpx8a9XH/f2b1ff4c261ed311ea989c17/

[jenkinmt]

Hi, I checked and I do not have that zip file of cytofkit2 in my var folder On Jul 28, 2021, at 12:48 PM, raman91 ***@***.******@***.***>> wrote: Hi, can you check the output path if there is a zip file of cytofkit ? : /var/folders/3n/cx37cm9d6_725ym8brb2r2yw0000gn/T//Rtmpx8a9XH /var/folders/3n/cx37cm9d6_725ym8brb2r2yw0000gn/T//Rtmpx8a9XH/f2b1ff4c261ed311ea989c17/ — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FJinmiaoChenLab%2Fcytofkit2%2Fissues%2F36%23issuecomment-888500249&data=04%7C01%7Cmatthew.t.jenkins%40vanderbilt.edu%7Cdcef5e0ea5294460006108d951efd917%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637630912851074484%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=kcOKLGLszA%2BWDLGyQc9msI5QXtVd8FpjqDjrtXBXczg%3D&reserved=0>, or unsubscribe<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FASTAD4ZNKPTAAW5DWMPG4O3T2A7FFANCNFSM5BBABBXA&data=04%7C01%7Cmatthew.t.jenkins%40vanderbilt.edu%7Cdcef5e0ea5294460006108d951efd917%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637630912851084477%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=fpdqBOp3E%2BlkpeznIxiKTFJtGmgP3Lq9Qsj8d7MANkk%3D&reserved=0>.

[jenkinmt]

Update: I am able to make tSNE and UMAP plots now it seems. However, I still do get the initial error mentioned above for $PnR value and truncation (I've tried setting truncation_max_range = FALSE already). Here were the lines of code I used to get the data sets (I had to do a force install since cytofkit2 is not on bioconductor. to get the UMAPs and tSNEs to work, I had to add these additional code lines:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")

BiocManager::install("IRanges")

and

if (!require("processx")) {
install.packages("processx", dependencies = TRUE)
library(processx)
}

[jenkinmt]

Also, the data store in my /var/folders under Rtmp files instead of where I direct them to via the gui

[raman91]

Thanks for the feedback. We will fix this and inform you