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t-SNE in R

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mleipold

Guru

Posts: 5796

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Mon Nov 06, 2017 5:21 pm

Re: t-SNE in R

Hi cytofkit maintenance team,

Thanks for the update! I'm glad that you and Erin were able to find and solve the issue.

One question: in the Github bug report thread (linked in your post; also: https://github.com/JinmiaoChenLab/cytofkit/issues/11), Erin comments that "For any users reading this, you can check your version with: packageVersion("cytofkit")"

You also comment that "It was not an issue in previous versions because before 1.8.3, the expression data for the markers of interest was being extracted in a previous step (specifically in cytof_exprsMerge), and therefore exprs_data was already filtered when passed to cytof_cluster"


When I checked packageversion in RStudio, it told me I currently have v1.4.10 (not sure whether it's bc I downloaded it when it first came out long ago, or whether it's a dependencies issue with my R version, etc).

Would this bug affect v1.4.10, or was it really only a v1.8.3 problem? The clusters I recently got in Phenograph with v1.4.10 didn't obviously look wrong/random.....


Mike
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ErinSimonds

Master

Posts: 50

Joined: Tue May 13, 2014 8:04 pm

Post Mon Nov 06, 2017 5:34 pm

Re: t-SNE in R

Hey Mike,

Only version 1.8.3 has the bug, so you should be OK. Users that installed cytofkit via Bioconductor between April 2017 and October 2017 are likely affected and should definitely upgrade. Really, everyone should upgrade.

Cytofkit users: If you want to find out if you were hit with the bug before you upgrade, you can run this command in R:

  Code:
packageVersion("cytofkit")"

...if the output says 1.8.3, then any results you obtained with that version of cytofkit had bad clusters . Sorry for the bad news. Thanks to the cytofkit dev team for implementing a patch so quickly after this bug was discovered.

ES
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