Pluritest for pluripotency broken

Question

[yassine]

Hi,

I am trying to run Pluritest with RNA-seq data with no success. The website from the github page is not up and so I went to the project forlder to run the script from there but there seem s to be a lot of inconsistencies related to commented code use for microarray. For example "arraydata" is no longer declared at the beginning but still is needed in all the try blocks in "clean_pluritest_RNA.R". Does anyone here have any experience using this test or can point me to where I can have a more recent version of it? I also found this version here but this looks like only an update on the code for microarray data.

Thank you.

Answer 1

[Roy]

Hi, The Pluritest web site should be working with RNAseq (was working fine over the weekend, yesterday). Please try again via the filezilla input method. I recommend keeping the batches of data to ~3 or 4 samples to not overwhelm the modest AWS server working in the background.

Cheers, Roy Williams

[yassine]

Thank you for your reply. I was actually referring to the link from the guthub page without realising it was actually the same website. However the problem remains, because of privacy related laws I am not allowed to upload this data on the website. I was hopong to be able to run "clean_pluritest_RNA.R" locally but it is not clear to me why the "arraydata" was commented out while being necessary for the rest of the script and where I can include my data. My understaing is that Pluritest needs Fastq files but I didn't see anything related to that in the script. Thank you for any clarifications you may have regarding this.

Cheers,

[DGTool]

Hi, just a question, were you able to find a way to get it to work locally? My understanding from looking around seems to be at least so far is that you cannot run PluriTest-RNA-seq locally, only through uploading it via the FTP server and having it analysed remotely.