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
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