[BioC] VSN: minimum number of controls?

[Eric E. Snyder]

Martin Morgan wrote:
> On 04/02/2010 02:41 PM, Eric E. Snyder wrote:
>> In my first project with R and BioConductor, I am analyzing some small
>> microarrays, starting with variance normalization with vsn.  Using
>> Wolfgang Huber's VSN.pdf tutorial I was able to do the exercise with the
>> "kidney" dataset without trouble.  However, when trying to run:
>>
>>>  fit = vsn2( noDNAcontrols )
>> Error in .local(x, reference, strata, ...) :
>>   One or more of the strata contain less than 42 elements.
>> Please reduce the number of strata so that there is enough in each stratum.
> 
> Always good to provide sessionInfo() so that we know the details of the
> software you're using

Okay, my sessionInfo:

> sessionInfo()
R version 2.10.1 (2009-12-14)
x86_64-unknown-linux-gnu

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] vsn_3.14.0    Biobase_2.6.1

loaded via a namespace (and not attached):
[1] affy_1.24.2          affyio_1.14.0        grid_2.10.1
[4] lattice_0.17-26      limma_3.2.1          preprocessCore_1.8.0

> and then good to try for a reproducible example, or at least enough info
> for other to reproduce your error. I started with example(vsn2) and then
> 
>> vsn2(kidney[1:20,])
> Error in vsnMatrix(exprs(x), reference, strata, ...) :
>   One or more of the strata contain less than 42 elements.
> Please reduce the number of strata so that there is enough in each stratum.
> 
> My guess is that noDNAcontrols is a matrix-like object with rows and
> columns transposed, i.e., samples x features rather than features x
> samples. What is class(noDNAcontrols) and dim(noDNAcontrols) ? Might as
> well copy and paste the output directly from R

> dim(noDNAcontrols)
[1]   6 853

> noDNAcontrols
          X1   X2   X3   X4 ... X853
no_DNA4 9840 5193 4854 6466 ... 6121
no_DNA5 5244 3569 3419 4587 ... 3595
no_DNA6 4630 3271 2877 5270 ... 2729
no_DNA3 4403 3782 3368 6004 ... 1557
no_DNA1 3745 4984 2842 6701 ...  783
no_DNA2 2099 4230 3165 6777 ...  756

[ellipsis provided by me and vi]

This is the data that vsn2() gags on.  Since the vsn2( kidney[1:20,] )
example also fails, it looks like vsn2() has a pretty strict requirement
for minimum sample size.  If so, why is that and is there any way around it?

I hope I have supplied enough information to work on now; it you need
anything else. please ask.

Many thanks!

As for my second question concerning the behavior of rnorm(), I should
probably simplify matters and resubmit it under a separate subject line.

Cheers,
eesnyder
-- 
Eric E. Snyder, Ph.D.
Virginia Bioinformatics Institute
Virginia Polytechnic Institute and State University
Blacksburg, VA 24061-0447
USA

Email:    eesnyder at vbi.vt.edu
JDAM:    N 37 12'01.6", W 80 24'26.9"