Anjan Purkayastha wrote:
> let me modify a local version and see the results. is it ok if i
> on this problem with you? i think dr. huber's method to genomic dna
> hybridization based approach suits our purpose the best.
> to give you a brief idea about our platform: we have built a whole
> genome tiling array for the vaccinia virus (ds DNA virus, genome
> ca 190kb); there are about 19000 overlapping probes, 60 bp in
> for each strand. for the purposes of normalization i have removed
> overlapping probes and am left with 6488 non-overlapping, contiguous
> anyway, i'll rerun the procedure with the revised script and see
> i come up with .
> thank you for your help.
> warm regards,
> Joern Toedling wrote:
>> looking at the source code of the function normalizeByReference,
>> 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
>> 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
>> you will have to work with a thus modified local copy of the
>> Sorry for the inconvenience.
>> Anjan Purkayastha wrote:
>>> thanks. i've solved the problem by wrapping an as. integer
>>> around the pm_vector. so here is my command:
>>> vac_normalized_data= normalizeByReference(vac_exp_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
>>> 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
>>> 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
>>> 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
>>> does not make much sense to me.
>>> if i understand the second part of the error message about
>>> strata correctly, there are less than 5000 features in some
>>> 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?
anjan purkayastha, phd
whitehead institute for biomedical research
nine cambridge center
cambridge, ma 02142
purkayas [at] wi [dot] mit [dot] edu