I'm trying to use the mva functions dist & hclust
however after a while I get the following message:
TypVSNdist <- dist(typVSN, method = "euclidean", diag = FALSE, upper =
FALSE)
Error: cannot allocate vector of size 589776 Kb
> typVSNcluster <- hclust(dist(typVSN@h))
Error: cannot allocate vector of size 589776 Kb
I'm running R in linux, any help much appreciated
regards
Jason
Dear Jason,
We would need to know a bit more about your settings,
like what one get by doing 'dim(typVSN)' or 'object.size(typVSN)',
and also the amount of RAM your machine has....
Hopin' it helps,
Laurent
On Thu, Mar 20, 2003 at 06:16:38PM +0000, Jason Skelton wrote:
>
>
> I'm trying to use the mva functions dist & hclust
> however after a while I get the following message:
>
> TypVSNdist <- dist(typVSN, method = "euclidean", diag = FALSE, upper
=
> FALSE)
> Error: cannot allocate vector of size 589776 Kb
>
> > typVSNcluster <- hclust(dist(typVSN@h))
> Error: cannot allocate vector of size 589776 Kb
>
> I'm running R in linux, any help much appreciated
>
> regards
>
> Jason
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
--
--------------------------------------------------------------
currently at the National Yang-Ming University in Taipei, Taiwan
--------------------------------------------------------------
Laurent Gautier CBS, Building 208, DTU
PhD. Student DK-2800 Lyngby,Denmark
tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent
Hi
The files I'm trying to run through hclust etc have the following
sizes
are these sizes "normal" for the output from vsn ?
MalVSN and typVSN are four slide experiments each with 12288 spot
features
YeastVSN is from one slide with 12288 features
> object.size(MalVSN)
[1] 984976
> object.size(typVSN)
[1] 984976
> object.size(YeastVSN1)
[1] 381904
each one returns the following message
Error: cannot allocate vector of size 589776 Kb
Unfortunately I'm not sure of the specifcations of the machine I'm
running
it from (Dec Alpha) and my systems administration group aren't
forthcoming apologies if this doesn't help much
Thanks for everyones help
Jason
On Fri, 21 Mar 2003, Laurent Gautier wrote:
>and also the amount of RAM your machine has....>
> > TypVSNdist <- dist(typVSN, method = "euclidean", diag = FALSE,
upper =
> > FALSE)
> > Error: cannot allocate vector of size 589776 Kb
> > > typVSNcluster <- hclust(dist(typVSN@h))
On Mon, 24 Mar 2003, Jason Skelton wrote:
> The files I'm trying to run through hclust etc have the following
sizes
Hi Jason,
You probably want to reduce the number of genes from 12488 to
something
like a few hundred before clustering. With 10^4 genes the distance
matrix
(which needs to be calculated as an intermediate step by hclust) has
size
of 10^8, which corresponds to roughly 1 Gigabyte. I would not expect
that
all 12488 rows of your data carry relevant information, esp. if you
have
only 4 conditions.
Also, it could be hard to display the cluster carpet or heatmap with
more
than a few hundred rows since your display may not have that many
pixels.
Best regards
Wolfgang
Hi Jason,
How big is your data matrix?
Best regards
Wolfgang Huber
On Thu, 20 Mar 2003, Jason Skelton wrote:
>
> I'm trying to use the mva functions dist & hclust
> however after a while I get the following message:
>
> TypVSNdist <- dist(typVSN, method = "euclidean", diag = FALSE, upper
=
> FALSE)
> Error: cannot allocate vector of size 589776 Kb
>
> > typVSNcluster <- hclust(dist(typVSN@h))
> Error: cannot allocate vector of size 589776 Kb
>
> I'm running R in linux, any help much appreciated
>
> regards
>
