[BioC] vsn in BioConductor 1.2

[White, Charles E WRAIR-Wash DC]

I spent the weekend getting to know this program better than I wanted
<grin>, but I probably still don't know it well enough. The fool's gold of
my wisdom is as follows: 

1) I would seriously consider reducing the amount of data you feed this
program. It took 4.5 hours to process a 15,552 x 38 matrix on a 1.2 GHz
Pentium III. There is a reason why the function vsnh exists. Unless you have
some serious GHz, you probably want to run vsn on a random sample of genes
or on one array at a time. 

2) Assuming that you are using data from a two channel microarray, I
strongly suspect that the red and green channels need to be side by side in
your matrix. I think the point is to quantify measurement variation without
contamination from any unnecessary source. I don't see any other way that
pair information is being passed to vsn.

3) I think that your problem and my old problem are likely to be quite
different. I fed the program data in a format it didn't understand and you
probably fed the program more data than it could process in a reasonable
amount of time. (Since the program doesn't use "much" memory, you wouldn't
have heard the hard drive running even if the program was still running.) 

4) I am pleased with the results I'm now getting from vsn. My initial
problems with this program were related to how I understand the
relationships between data elements and Bioconductor objects verses what
appears to be a somewhat different relationship in vsn.

-----Original Message-----
From: Isaac Neuhaus [mailto:isaac.neuhaus at bms.com] 
Sent: Monday, July 21, 2003 1:37 PM
To: w.huber at dkfz-heidelberg.de
Cc: White, Charles E WRAIR-Wash DC; 'bioconductor at stat.math.ethz.ch'
Subject: Re: [BioC] vsn in BioConductor 1.2

Hi Wolfgang:

I am also getting the same error with a matrix that is 4992 x 376. Here 
are the R commands:

 > data <- read.table("file.msk", header=T, sep = "\t", row.names=1)
 > data <- as.matrix(data)
 > vsn.data <- vsn(data)
vsn is working on a 4992 x 376 matrix, with lts.quantile=0.5; please 
wait for 11 dots:
.

and then dies. Any suggestions?

after I do a traceback I get the following:

 > traceback()
2: optim(par = p0, fn = ll, gr = grll, method = "L-BFGS-B", control = 
control,
       lower = plower)
1: vsn(data)

Any help is greatly appreciated.

Isaac


w.huber at dkfz-heidelberg.de wrote:....