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mehrnoushmalek / DuraClone-gating

Automated gating of Basic and Bcell panel of DuraClone
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Error in tail(getPeaks(x, channels.ind["FS-W"], tinypeak.removal = 0.4)$Peaks, : could not find function "getPeaks" #1

Open xigyou opened 4 years ago

xigyou commented 4 years ago

I get the follow problem.

could not find function "getPeaks"

the Detail info is:

root@227e9090a531:/# Rscript /project/software/DuraClone-gating/Run_automated.R Loading required package: methods Warning message: no DISPLAY variable so Tk is not available [1] "/flowRepositoryExperimentDownloaded/Fortessa vs. Navios/sample/Navios" Warning message: In dir.create(paste(output.path, dataset, "Results", type, sep = "/"), : '/project/PathToSaveTheResults/Fortessa vs. Navios/Results/Navios' already exists [1] 3 [1] "/flowRepositoryExperimentDownloaded/Fortessa vs. Navios/sample/Navios" [1] NA [1] "Sample 3 FortvsNavios Basic YVR_RG 00003744 2018-06-28.LMD" Error in tail(getPeaks(x, channels.ind["FS-W"], tinypeak.removal = 0.4)$Peaks, : could not find function "getPeaks" Calls: source ... fsApply -> structure -> lapply -> FUN -> FUN -> tail Execution halted

mehrnoushmalek commented 4 years ago

Hey,

getPeaks is a function in flowDensity package, so either it's not installed properly, or you have a very old version.

xigyou commented 4 years ago

Hey,

getPeaks is a function in flowDensity package, so either it's not installed properly, or you have a very old version.

This is my version, which version is needed?

packageVersion("flowDensity")
[1] '1.10.0'

mehrnoushmalek commented 4 years ago

I don't know about version 1.10.0 as it's very old, right now it's 1.20 in Bioconductor: https://bioconductor.org/packages/release/bioc/html/flowDensity.html I would suggest installing >1.17.

xigyou commented 4 years ago

Thank you very much, and I how you could tell me the R version and the operating system version you use. because the flowDensity is really hard to install.

Thank you again.

mehrnoushmalek commented 4 years ago

It's not flowDensity, you need to make surergeos, sp are installed properly before installing flowDensity, it's in the DESCRIPTION file of flowDensity. We used Linux, and R version won't matter, but anything after 3.4 would do the job. I would recommend installing flowDensity from github (using devtools package), so you have the recent version.

xigyou commented 4 years ago

OK, Thank you very much! and I will try it.

mehrnoushmalek commented 4 years ago

Hello @xigyou, is your problem solved?