FAQ  •  Register  •  Login

Cytofkit

Forum rules
Please be as geeky as possible. Reference, reference, reference.
Also, please note that this is a mixed bag of math-gurus and mathematically challenged, so choose your words wisely :-)
<<

claudechew

Participant

Posts: 10

Joined: Tue Nov 04, 2014 5:13 pm

Post Mon Oct 08, 2018 2:59 pm

Re: Cytofkit

I too am having this issue with no tsne parameters being generated. My versions for Flowcore and cytofcore are as follows:

Flowcore 1.11.0

Cytofkit 1.12.0
<<

nkhanbham

Master

Posts: 53

Joined: Wed Feb 25, 2015 3:03 pm

Post Tue Oct 09, 2018 7:22 pm

Re: Cytofkit

Further to my issues with Cytofkit output files; I installed the latest version of flowCore using the code shared earlier (many thanks to Samuel G). This prompted a requirement for installing Rtools. This was a lengthy process but it seems to have everything working now. FCS files generated have the tSNE and phenograph channels and I can play with the data in FlowJo. Happy days.
<<

sgranjeaud

Master

Posts: 123

Joined: Wed Dec 21, 2016 9:22 pm

Location: Marseille, France

Post Tue Oct 09, 2018 7:56 pm

Re: Cytofkit

@Naeem thanks for sharing and confirming it works
@Claude your packages seems to be out dated. IMHO you should update your R installation.
<<

claudechew

Participant

Posts: 10

Joined: Tue Nov 04, 2014 5:13 pm

Post Wed Oct 10, 2018 2:38 pm

Re: Cytofkit

Updated my flowCore package to 1.47.9 and re-ran the pipeline and still no tsne and phenograph parameters, any ideas?
<<

claudechew

Participant

Posts: 10

Joined: Tue Nov 04, 2014 5:13 pm

Post Wed Oct 10, 2018 2:47 pm

Re: Cytofkit

Nevermind my last response, I am using FCSExpress and after looking at the keywords, realized that cytofkit had indeed created the tsne1 and tsne2 and Phenograph parameters, but that I had to change the options in FCSExpress to use the "Name" keyword as the parameter name instead of "Stain" which it tries to read by default.
<<

Nrosine

Participant

Posts: 3

Joined: Wed Nov 14, 2018 12:20 pm

Post Thu Nov 15, 2018 5:32 pm

Re: Cytofkit

Hi everyone!

I'm new user of cytofkit.
I have a naive question about the scale you see on the top left of the heatmaps generated.
On Y axis you have « count » on the x axis you have « value « and you have this blue curve inside.
Can you tell me to what they correspond please?

Thank you!
<<

Nrosine

Participant

Posts: 3

Joined: Wed Nov 14, 2018 12:20 pm

Post Mon Dec 31, 2018 4:45 pm

Re: Cytofkit

Hi everybody

Does anyone ever use cytofkit on data from Sony spectral analyzer?
Does the transformation of the data is the same? Autolgcle or cytofAsinh?

Cheers
<<

nkhanbham

Master

Posts: 53

Joined: Wed Feb 25, 2015 3:03 pm

Post Mon Feb 11, 2019 5:42 pm

Re: Cytofkit

We are now having problems in Cytofkit with the change in code post-Bioclite deprecation.

Previously we were using the following (and it worked)

source("https://bioconductor.org/biocLite.R")
biocLite("cytofkit")
install.packages("devtools")
devtools::install_github("RGLab/flowCore", ref = "trunk")
library("cytofkit")
cytofkit_GUI()

We have tried the new code from Bioconductor :

if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("cytofkit", version = "3.8")

then

library("cytofkit")


There are multiple dependencies that flag up (Rccp, httpuv, BiocParallel, colorspace, ggplot2 which require separate installation. In the end the GUI command doesnt work.

cytofkit_GUI()
Error in cytofkit_GUI() : could not find function "cytofkit_GUI"

Its isnt clear whether we need more code in after the cytofkit install code before running the GUI command.

Can anyone help please?
NK
<<

dtelad11

Master

Posts: 129

Joined: Mon Oct 31, 2016 6:26 pm

Post Mon Feb 11, 2019 5:48 pm

Re: Cytofkit

Could you please run

BiocManager::install("cytofkit", version = "3.8")

Then copy and paste all of the resulting output here:

https://www.hastebin.com/

Once you do it will give you a link (the browser title bar will change). Could you please copy and paste that link here? That will allow others to review the exact errors.
<<

nkhanbham

Master

Posts: 53

Joined: Wed Feb 25, 2015 3:03 pm

Post Mon Feb 11, 2019 6:02 pm

Re: Cytofkit

Thanks El-ad. Here is the new link

https://www.hastebin.com/uduwulagew.coffeescript.
PreviousNext

Return to CyTOF data analysis

Who is online

Users browsing this forum: No registered users and 14 guests

cron