[BioC] Calculation times

[A.J. Rossini]

might be a known problem with R 1.7.0 and recent R 1.7.0-patched
(until a few days ago).  Install a very recent version of R-patched
(today or later) might help., or wait until 1.7.1 (to be released
soon). 

"Claire Wilson" <ClaireWilson at picr.man.ac.uk> writes:

> Dear all,
>
> I have recently upgraded my linux machine from R1.6.2/Bioconductor 1.1 to R1.7/Bioconductor 1.2 and have found that the new version runs considerabley slower than the old version. So much so that I have a function to calculate fold change for an expression set that takes a few minutes to run in R1.6.2/BioC 1.1, but well over half an hour to run on the latest version. 
>
> here is the code..
>  calc.fc <- function(y, x) {
> 	  # split y according to treatment
>     	     exprs.values <- split(y, treatment)
> 	  # exprs.values has 2 elements control in [[1]] and treatment in [[2]]
> 	  # exprs.values[[1]][1:3] is the control group for a
> 	  # exprs.values[[1]][4:6] is the control group for b
> 	  # exprs.values[[2]][1:3] is the treatment group for a
> 	  # exprs.values[[2]][4:6] is the treatment group for b
>     if (x == "a") {
>         # Calculate the means expression level for each group in a
>            m1 <- log2(mean(exprs.values[[1]][1:3]))
>            m2 <- log2(mean(exprs.values[[2]][1:3]))
>     }else{
>        # Calculate the means expression level for each group in b
>           m1 <- log2(mean(exprs.values[[1]][4:6]))
>           m2 <- log2(mean(exprs.values[[2]][4:6]))
>      }
>     # Calculate the fold change
>        log.fold.change <- m1 - m2
>     # If it is less than 0 it is a negative fold change
>     # Need to make it positive, take the anti-log and then make it negative again
>     # Else just calculate the anti-log
>       if (log.fold.change < 0 ) {
>           x <- -1 * log.fold.change
>           fold.change <- -1 * (2^x)
>       }else {
>           fold.change <- (2^log.fold.change)
>       }
>       return (t(fold.change))
>   }
>   
> # Run the function
>  esApply(eset,1,calc.fc, x="a")
>
> Any ideas?
> Thanks
>
> claire
> --
> Claire Wilson   
> Bioinformatics group  
> Paterson Institute for Cancer Research  
> Christies Hospital NHS Trust  
> Wilmslow Road,  
> Withington  
> Manchester  
> M20 4BX  
> tel: +44 (0)161 446 8218  
> url: http://bioinf.picr.man.ac.uk/
>  
> --------------------------------------------------------
>
>  
> This email is confidential and intended solely for the use of th... {{dropped}}
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>

-- 
A.J. Rossini  /  rossini at u.washington.edu  /  rossini at scharp.org
Biomedical/Health Informatics and Biostatistics, University of Washington.
Biostatistics, HVTN/SCHARP, Fred Hutchinson Cancer Research Center.
FHCRC: 206-667-7025 (fax=4812)|Voicemail is pretty sketchy/use Email 

CONFIDENTIALITY NOTICE: This e-mail message and any attachments ... {{dropped}}