cnSegmentation for EPICv2 data
SteffanChristiansen opened this issue · comments
It seems like there are no default reference data for the EPICv2 platform for SeSAMe v. 1.20.0.
sdf <- openSesame(searchIDATprefixes(data_dir), manifest = addr, func = NULL, prep = "", platform = "EPICv2")
segs <- cnSegmentation(sdf[[1]])
Error in cnSegmentation(sdf[[1]]) :
Please provide sdfs.normal=. No default for EPICv2
Do you plan any updates to include that in the near future or do you know a suitable reference that you can recommend for the task of identifying copy number segments in a tumor cell line?
Yes, the reference has been added to v.1.21.x. See also the following #129 for previous versions.
Thanks for the suggestion. I will let you know when I have tested the solution. Unfortunately, I am facing the same issue as described in #145 and in #127 described by @bethan-mallabar-rimmer.
Have you tried upgrading sesameData, or do you have problem mainly with caching?
Yes, I removed the cache dir, upgraded to sesameData and SeSAMe v 1.21 (or above) cached again. Still, I was not able to cache all of the data as described in #145 .
Returned to version 1.20 afterwards as I was no longer able to run several of the functions.
Yes, I removed the cache dir, upgraded to sesameData and SeSAMe v 1.21 (or above) cached again. Still, I was not able to cache all of the data as described in #145 .
Returned to version 1.20 afterwards as I was no longer able to run several of the functions.
@SteffanChristiansen @zwdzwd @HenrikBengtsson @karltk I am having this same problem. When I upgrade Sesame to developer version to use defaults for Epic V2, the cache stops to work making many other functions to fail.
Yes, I removed the cache dir, upgraded to sesameData and SeSAMe v 1.21 (or above) cached again. Still, I was not able to cache all of the data as described in #145 .
Returned to version 1.20 afterwards as I was no longer able to run several of the functions.@SteffanChristiansen @zwdzwd @HenrikBengtsson @karltk I am having this same problem. When I upgrade Sesame to developer version to use defaults for Epic V2, the cache stops to work making many other functions to fail.
I'm also having a DataCache issue. Just wondering if anyone has found a solution?