[BioC] tilingArray- normalizeByReference

[Anjan Purkayastha]

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 wrote:
> Hello Anjan,
>
> well, the error message indicates that your vector pm_vector is not
> usable by the function. Is it really an integer vector. What is the
> output of
> str(pm_vector)
> ?
> Probably, it would be better to read in the file by something like
> pm_vector <- read.delim("PerfectMatchIndex", skip=<put number of header
> lines here!>)$V1
> Again, check the result using
> str(pm_vector)
> If you want to use other functionalities of package tilingArray, you
> should consider creating a 'probeAnno' environment, which holds the
> mapping between probes and genomic match positions, for your array.
> Please see the script "makeProbeAnno.R" in the package's "scripts"
> directory for details. Once you have such a probeAnno object, the
> function "PMindex" can be used to obtain a numeric vector that you can
> use as "pm" in the normalization function.
> Please see the vignette "assessNorm" of package tilingArray for more
> details.
>
> Best regards,
> Joern
>
> Anjan Purkayastha wrote:
>   
>> hi all,
>> a rookie tilingArray question.
>> i'm having trouble creating the perfect match index vector.
>> for my probe set (n= 6490), each probe is a unique, perfect match to
>> its target.
>> i have created a probe index file that contains the integers: 1,
>> 2....6490 (one index per line).
>> i scanned this file as:  pm_vector <- scan("PerfectMatchIndex", 0)
>>
>> i used the pm_vector in a following command:
>> vac_normalized_exp_data <- normalizeByReference(vac_exp_set,
>> vac_hyb_set, pm= pm_vector, background= bg_vector, cutoffQuantile= 0)
>>
>> this gives me an error:
>> 'pm' must be an integer vector with values between 1 and 6490.
>>
>> any idea what the problem could be?
>> tia
>> anjan
>>
>>     
>
>   


-- 
===========================================
anjan purkayastha, phd
bioinformatics analyst
whitehead institute for biomedical research
nine cambridge center
cambridge, ma 02142

purkayas [at] wi [dot] mit [dot] edu  
703.740.6939