[BioC] pmindex in oligo package

[Gayla Olbricht]

Hi Benilton,

Thanks for the advice.

So, when I ran the first thing you suggested, I got the following error:

> xy.coord <- getPD(data_bpmap) [pmindex(data_bpmap), c("X", "Y")]
Error in getPD(data_bpmap)[pmindex(data_bpmap), c("X", "Y")] :
  object is not subsettable

But, was able to use your suggestion as a hint to get at the X,Y coordinates 
for PM values by the following:
feature<-getPD(data_bpmap)
PMxcoord<-feature$X[pmindex(data_bpmap)]
PMycoord<-feature$Y[pmindex(data_bpmap)]

This seems to give me what I need.

I'm still not exactly sure how the pmindex is calculated, but maybe the x,y 
coordinate information will be all I need.

I did try running the function i2xy and got the following:

> pmi <- pmindex(data_bpmap)
> xy.coord2 <- i2xy(pmi, data_bpmap)
Error: could not find function "i2xy"

The same thing happened when I tried "indices2xy" instead.

I would still be interested to know if the i2xy function can work, but I 
guess I can do without it since I have the x,y information.

Thanks again for your quick response and help with this!
-Gayla







----- Original Message ----- 
From: "Benilton Carvalho" <bcarvalh at jhsph.edu>
To: "Gayla Olbricht" <ghobbs at stat.purdue.edu>
Cc: <bioconductor at stat.math.ethz.ch>
Sent: Thursday, November 15, 2007 3:56 PM
Subject: Re: [BioC] pmindex in oligo package


> say "TilingFeatureSetObject" is your object, you should be able to get  X 
> and Y coordinates by:
>
> xy.coord <- getPD(TilingFeatureSetObject) 
> [pmindex(TilingFeatureSetObject), c("X", "Y")]
>
> i can't check right now, sorry, but i think there's an (unexposed) 
> function that should help you with that:
>
> pmi <- pmindex(TilingFeatureSet)
> xy.coord2 <- i2xy(pmi, TilingFeatureSet)
>
> let us know how these go and i'll get back to you ASAP.
>
> b
>
> On Nov 15, 2007, at 3:43 PM, Gayla Olbricht wrote:
>
>> Hello,
>>
>> I am using the oligo package to work with tiling arrays.
>>
>> I was wondering if there is a way to either:
>>
>> 1.  See how the pmindex function in oligo is calculating the indices?
>> or
>> 2.  Obtain the actual x,y coordinates for each probe?
>>
>> I found the functions indices2xy and xy2indices in the affy package,  but 
>> can't seem to find an equivalent function in oligo.
>>
>> Any advise would be greatly appreciated.  My session info is below,  in 
>> case it is helpful.
>>
>> Thanks!
>> -Gayla Olbricht
>>
>> _______________________
>>> sessionInfo()
>> R version 2.6.0 (2007-10-03)
>> x86_64-redhat-linux-gnu
>>
>> locale:
>> LC_CTYPE = en_US .UTF -8 ;LC_NUMERIC = C ;LC_TIME = en_US .UTF -8 
>> ;LC_COLLATE = en_US .UTF -8 ;LC_MONETARY = en_US .UTF -8 ;LC_MESSAGES = 
>> en_US .UTF -8 ;LC_PAPER = en_US .UTF -8 ;LC_NAME = C ;LC_ADDRESS 
>> =C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] splines   tools     stats     graphics  grDevices utils      datasets
>> [8] methods   base
>>
>> other attached packages:
>> [1] pd.at35b.mr.v04_1.0.0 oligo_1.2.1           oligoClasses_1.0.3
>> [4] affxparser_1.10.1     AnnotationDbi_1.0.6   preprocessCore_1.0.0
>> [7] RSQLite_0.6-3         DBI_0.2-4             Biobase_1.16.1
>>
>> loaded via a namespace (and not attached):
>> [1] rcompgen_0.1-15
>>
>> [[alternative HTML version deleted]]
>>
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>