Hello, my apologies for the sloppy post.

You can find a sample dataset here: https://www.dropbox.com/sh/p1od9e4vx8ky66a/igt2OkNDbQ

And the code I ran was essentially:

data       <- read.csv("subsample.csv",header=FALSE)
itemLabels <- t(read.csv("labels.csv", header=FALSE)) #read in and transpose
timePoints <- 1:24                                    #number of timepoints
BHC_OUT    <- bhc(data,itemLabels,timePoints,"time-course",verbose=TRUE,numThreads=8)

This is where it completely locks up. Also, note that I get the same result with multiple permutations of the bhc command, and that this occurs on multiple versions of R for me (including the latest releases).

I should note that I have demeaned and variance normalized all time series before entering them into bhc, if that makes a difference.

Cheers, Joseph

On Wed, Apr 24, 2013 at 3:56 PM, Joseph Viviano<vivianoj@yorku.ca>  wrote:

> <mailto:bioconductor@r-project.org>Hello all,
>
> I am having a great deal of trouble getting BHC to run on non-trivial
> datasets. I am using the following commands:
>
> data           <- read.csv("data.csv")

Can you share this dataset, or at least enough of it to reproduce the problem?

> itemLabels <- names(data)
> timePoints <- 1:24 # for the time-course case
>
> nDataItems <- nrow(data) # this equals 152000, approximately
> nFeatures  <- ncol(data)   # this equals 24
>
> BHC_OUT <- bhc(data,itemLabels,timePoints"time-course",verbose=TRUE)

This line produces a syntax error.

In order to help you we need a fully reproducible example. Also,
please send the output of the sessionInfo() command.

Dan


> ---
>
> This causes R to immediately lock up on windows 7, linux mint 13, and
> OSX 10.6.8. The input data are variance normalized time-series exported
> from MATLAB.
>
> Here is a sample timeseries from the .csv:
>
> -1.7858,-0.26742,0.37038,-0.87986,-0.55435,-0.89642,-1.2815,-0.62659,-0.98028,-1.0542,-1.0058,0.51103,0.90252,2.5272,-0.3048,0.81275,0.22414,0.15235,-0.20437,0.2545,0.95103,1.4214,0.82618,0.77179
>
> Any help would be greatly appreciated.
>
> Cheers, Joseph
>
>
>          [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:http://news.gmane.org/gmane.science.biology.informatics.conductor

_______________________________________________
Bioconductor mailing list
Bioconductor@r-project.org
https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives:http://news.gmane.org/gmane.science.biology.informatics.conductor


	[[alternative HTML version deleted]]

