Open mflamand opened 4 years ago
Hi, we develop a docker image that swaps xtail into R to solve this problem. You can see the manual from this link https://hub.docker.com/r/yanglab/xtail .
Thank you for the reply. Although this probably works great, using a docker is not the best option for me.
If you are interested in fixing the R code for R4.0, or anyone else want's to use it directly, I manage to make it work by doing the following changes:
CoreFuns.R#57 and CoreFuns#58 : add withDimnames=FALSE within assays() methods.R#19 : add withDimnames=FALSE within assays()
This worked by still gave warnings that DESeq2 converted strings to factors in the formula.:
changing xtail.R#48 with : condition=as.factor(condition) fixed those warnings.
The changes to factors are directly caused by the new data.frame behavior, but I am unsure why the SummarizedExperiment assay() behavior have changed.
In any case, running the sample data under R3.6.3 and 4.0.0 gave me the same number of log2FC and log2R
@mflamand your fix worked for me, thank you!
See #18
Hello, I tried to repackage xtail v1.1.5 under the newly released R4.0.0 (windows10) Unfortunately I running the main function xtails fails as such:
xtail still works on my system for R-3.6.3 so its not an urgent issue. I was wondering if you were planning to update the code to make compatible with version 4.x.x ? There were quite a few changes (such as the now default data.frame(stringsAsFactors = FALSE) )made so I am unsure were to start looking. If necessary I can also try under a different platform (RHEL or Fedora Linux) to see if the problem persist
Thanks for your help!