[BioC] tilingArray- normalizeByReference

[Joern Toedling]

Anjan,
looking at the source code of the function normalizeByReference, there
is indeed the line
vsnMatrix(xn, lts.quantile = 0.95, subsample = as.integer(2e+05)) ,
and since your matrix only has 6488 lines, this cannot work.
Without knowing more details about your array platform and study, I
cannot say whether or not the function "normalizeByReference" is really
applicable to your array platform. However, we should augment the
function anyway by chaning this line to something like
vsnMatrix(xn, lts.quantile = 0.95, subsample = min(nrow(xn),
as.integer(2e+05))) .
We are going to make this change and it will be included in the
development version of tilingArray within a few days. For the moment,
you will have to work with a thus modified local copy of the function.
Sorry for the inconvenience.

Regards,
Joern


Anjan Purkayastha wrote:
> joern,
> thanks. i've solved the problem by wrapping an as. integer function
> around the pm_vector. so here is my command:
>
> vac_normalized_data= normalizeByReference(vac_exp_set, vac_hyb_set,
> pm= as.integer(pm_vector), background= as.integer(bg_vector))
>
> however my story does not end here. i get a further set of errors
> after this command.
> Error in validObject(.Object) :
>  invalid class "vsnInput" object: 'subsample' must be a numeric vector
> of length 1 with values between 0 and 6488.
> In addition: Warning message:
> In normalizeByReference(vac_exp_set, vac_hyb_set, pm =
> as.integer(pm_vector),  :
>  'some strata of background contain fewer than 5000 features, are you
> sure this is alright?
> Error in exprs(vsnMatrix(xn, lts.quantile = 0.95, subsample =
> as.integer(2e+05),  :
>  error in evaluating the argument 'object' in selecting a method for
> function 'exprs'
>
> the first part of the error message: vsnInput" object: 'subsample'
> must be a numeric vector of length 1 with values between 0 and 6488,
> does not make much sense to me.
> if i understand the second part of the error message about background
> strata correctly, there are less than 5000 features in some background
> strata. that is understandable as i have only 1275 probes in the
> background set. there are a total of 6488 probes in my set.
>
> any ideas on how to troubleshoot this?
> thanks.
> anjan
>
>
>

-- 
Joern Toedling
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
United Kingdom
Phone  +44(0)1223 492566
Email  toedling at ebi.ac.uk