Hi Avehna

When I do this, I use limma to fit a model that includes every factor, and the resulting output has both a F statistic and an F statistic p-value.  These can be used to identify genes that are changing over any of your experiments

However, I often find that even if I use a very stringent multiple testing procedure, I still end up with 10000s of genes to worry about.  In my experience, this is not only difficult to visualise, but also to interpret.

In the past I have applied other filters, such as the magnitude of change over time; or perhaps the lab scientist who produced the data may have created a time course, but is specifically interested in particular time points, so I filter on those; or sometimes, I just take the top n most changing genes, whether n be 500, 1000, 2000 etc.

Thanks
Mick

From: avehna [mailto:avhena@gmail.com]
Sent: 18 March 2010 01:05
To: michael watson (IAH-C); Steve Lianoglou; bioconductor@stat.math.ethz.ch
Subject: Re: [BioC] hclust for 13000 genes

Hi again,

I'm using a very powerful computer (a Mac Pro) with a huge amount of memory and it's also very fast, that's why I wondered why this error came out. I think the problem is that I'm using R in 32 bit mode. How could I change it?

Regarding the amount of genes: For each treatment by separate the amount of genes is smaller, but since I'm interested in making a heatplot to visualize the gene profile across all treatments I'm using the union of all sets. I'm very open to new suggestions from you.

Thank you so much for your help,

Avhena
On Wed, Mar 17, 2010 at 6:09 PM, michael watson (IAH-C) <michael.watson@bbsrc.ac.uk<mailto:michael.watson@bbsrc.ac.uk>> wrote:
The first answers is that you need to make sure you computer has enough memory, and that R can access that memory.  See memory.size() and memory.limit() for answers.

The second answer is: are you *sure* you want to cluster 13,777 genes?  That's an awful lot to visualise and interpret.....
________________________________________
From: bioconductor-bounces@stat.math.ethz.ch<mailto:bioconductor-bounces@stat.math.ethz.ch> [bioconductor-bounces@stat.math.ethz.ch<mailto:bioconductor-bounces@stat.math.ethz.ch>] On Behalf Of avehna [avhena@gmail.com<mailto:avhena@gmail.com>]
Sent: 17 March 2010 21:59
To: bioconductor@stat.math.ethz.ch<mailto:bioconductor@stat.math.ethz.ch>
Subject: [BioC] hclust for 13000 genes

Hi There:

I'm trying to cluster 13777 genes that are differentially expressed across
three different treatments but I'm getting the following error:

------------------------------------------------
R(32949) malloc: *** mmap(size=1518448640) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
Error: cannot allocate vector of size 1.4 Gb
Execution halted
-------------------------------------------------

I wonder how could I fix it in order to get the clusters and the heatmap
with the expression profile. I would appreciate any suggestion from you!.

Thank you so much for your help in advance,

Avhena
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