Question: FlowCore and FlowTrack installation and running problems
0
gravatar for angela.oliveira.pisco
3.8 years ago by
European Union
angela.oliveira.pisco0 wrote:

Hi,

I'm new to R and I'm facing some problems.

I'm trying to install FlowCore and FlowTrack and it's not working.

I manage to run FlowCore:

> pkg <- "/private/var/folders/7h/h3fq1kf54rjgs6v_l6jhbjcc0000gn/T/RtmpJGC7dK/downloaded_packages/flowCore_1.34.3.tgz"
> install.packages(pkg, repos=NULL, type="source")
* installing *binary* package ‘flowCore’ ...
* DONE (flowCore)
> library(flowCore)
>    data(GvHD)
>    class(GvHD)
[1] "flowSet"
attr(,"package")
[1] "flowCore"
> GvHD
A flowSet with 35 experiments.

An object of class 'AnnotatedDataFrame'
  rowNames: s5a01 s5a02 ... s10a07 (35 total)
  varLabels: Patient Visit ... name (5 total)
  varMetadata: labelDescription

  column names:
  FSC-H SSC-H FL1-H FL2-H FL3-H FL2-A FL4-H Time

but then

tmixGate <- tmixFilter(parameters=c("FSC-H","SSC-H"), K=1)
Error: could not find function "tmixFilter"

> biocLite("flowTrack")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.2), R version 3.2.0.
Installing package(s) ‘flowTrack’
Warning message:
package ‘flowTrack’ is not available (for R version 3.2.0) 
> packageVersion('mgcv')
[1] ‘1.8.6

when I check in the the /download_packages folder I have no flowTrack_x file at all...

I really appreciate if you could help me sorting this out.

Thanks,

Angela

 

 

 

 

 

flowcore flowtrack • 917 views
ADD COMMENTlink modified 3.8 years ago by Dan Tenenbaum8.2k • written 3.8 years ago by angela.oliveira.pisco0

'tmixFilter' belongs to 'flowClust' package and you need to install that using 'biocLite' as Dan suggested. 

ADD REPLYlink written 3.8 years ago by Jiang, Mike1.2k
Answer: FlowCore and FlowTrack installation and running problems
0
gravatar for Dan Tenenbaum
3.8 years ago by
Dan Tenenbaum8.2k
United States
Dan Tenenbaum8.2k wrote:

You should be using biocLite() to install all packages, not downloading packages and then installing them with install.packages()

As far as flowTrack is concerned, it looks like that package was written for a course that used R-2.11 and it may not work properly in newer versions of R. Note that flowTrack is not an official Bioconductor package. 

If you are trying to learn about flow cytometry in R/Bioconductor I recommend instead starting with Flow Cytometry and other assays which is more current and known to work under the current Bioconductor release version.  Flow experts who read this may have other tips.

Read on only if you REALLY need flowTrack.

I was able to install flowTrack like this:

source("http://bioconductor.org/biocLite.R")
courseRepos <- "http://bioconductor.org/course-packages"
allRepos <- c(courseRepos, biocinstallRepos())
install.packages("flowTrack", type="source", repos=allRepos)

Note that flowTrack is so old that it isn't using the proper vignette directory so you can't see its vignettes with browseVignettes("flowTrack");  you will need to do this:

download.packages("flowTrack", '.', repos=allRepos, type="source")

Then quit R and do this at the command prompt:

tar zxf flowTrack_0.1.0.tar.gz
open flowTrack/inst/doc/*.pdf

 

 

 

ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by Dan Tenenbaum8.2k
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