Open hanketim opened 10 months ago
Hi @hanketim,
Thanks for reporting this issue: it arose from R not allowing more than one condition in an if statement. I fixed the issue in DecompPipeline with the most recent commit. Please try to update DecompPipeline and let us know if it works afterwards!
Best,
Michael
Dear @schmic05 ,
thank you very much for your quick and helpful reply. That solved the problem and the confounders were removed! Now I can start with the methylome deconvolution, I am very excited!
Best regards, Tim
I want to use the script for MeDeCom with my own 76 samples. Up to the removal of the confounder by means of ICA everything worked without problems. I worked with DecompPipeline 1.0.3 and MeDeCom 1.0.1 This is the code I used:
data.prep <- prepare.data(rnb.set=data.prep$rnb.set.filtered, normalization = "none", analysis.name = "Glioblastoma", filter.beads = FALSE, filter.intensity = FALSE, remove.ICA = TRUE, filter.na = FALSE, filter.context = FALSE, filter.snp = FALSE, filter.sex.chromosomes = FALSE, filter.cross.reactive = FALSE, conf.fact.ICA = c("Geschlecht","AlterbeiED"), ica.setting = c("alpha.fact"=1e-5,"save.report"=TRUE, "ntry"=10,"nmin"=20,"nmax"=50,"ncores"=15))
however now the following error occurs:
Analyse stability Starting parallel calculation on 10 core(s)... System: unix 50 components, 10 runs, 518989 features, 76 samples. Start time: 2023-10-26 18:35:31.038152 Done! End time: 2023-10-26 19:06:30.023182 Time difference of 30.98308 mins Calculate ||X-SxM|| and r2 between component weights Correlate rows of S between tries Build consensus ICA Analyse stability
Error in if (!fact %in% names(Var)) { : the condition has length > 1
For me it looks like 50 components are loaded (nmax = 50), but after that a problem occurs, which i don't understand. I would be very grateful for any help. If further information / details are needed, I will of course gladly provide them.