Hi Benilton and all,

Thanks for kind suggestions. I am eager to try crlmm with 2 samples, but error message "Error: number of cluster centres must lie between 1 and nrow(x)". Details were shown below. Any further suggestions will be appreciated. J.

Error: number of cluster centres must lie between 1 and nrow(x)

> celFiles
[1] "/tmp/data//00-0523B_SNP_6-0.CEL" "/tmp/data//02-0476B_SNP_6-0.CEL"
> crlmmResult <- crlmm(celFiles)

crlmmResult <- crlmm(celFiles)
Loading annotations and mixture model parameters.
Processing 2 files.
  |======================================================================| 100%
Loading annotations.
Determining gender.
Error: number of cluster centres must lie between 1 and nrow(x)
> 
> sessionInfo()

sessionInfo()
R version 2.13.2 (2011-09-30)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] genomewidesnp6Crlmm_1.0.4 crlmm_1.10.0             
[3] oligoClasses_1.14.0       Biobase_2.12.2           

loaded via a namespace (and not attached):
 [1] affyio_1.20.0         annotate_1.30.1       AnnotationDbi_1.14.1 
 [4] Biostrings_2.20.4     bit_1.1-7             DBI_0.2-5            
 [7] ellipse_0.3-5         ff_2.2-3              genefilter_1.34.0    
[10] IRanges_1.10.6        mvtnorm_0.9-9991      preprocessCore_1.14.0
[13] RSQLite_0.10.0        splines_2.13.2        survival_2.36-9      
[16] xtable_1.6-0         
> 
> 



________________________________
From: Benilton Carvalho <beniltoncarvalho@gmail.com>
To: cstrato <cstrato@aon.at>
Cc: James W. MacDonald <jmacdon@med.umich.edu>; "Bioconductor@r-project.org" <Bioconductor@r-project.org>
Sent: Wednesday, October 19, 2011 5:25 PM
Subject: Re: [BioC] SNP 6 chip

for 250K, you can genotype with the CRLMM algorithm in oligo.

for SNP 6.0, use the crlmm package instead... the implementation
currently available there is an upgrade of the one in oligo, using
features exclusive for SNP 6.0... the crlmm package also offers a CN
tool (details on the vignette).

b

On 19 October 2011 22:12, cstrato <cstrato@aon.at> wrote:
> Dear Jim,
>
> Thank you for mentioning xps, however xps does only work for expression
> arrays and not for mapping arrays such as SNP6.
>
> Best regards
> Christian
>
>
> On 10/19/11 10:51 PM, James W. MacDonald wrote:
>>
>> Hi John,
>>
>> On 10/19/2011 2:27 PM, John linux-user wrote:
>>>
>>> Hello,
>>>
>>> Can you please suggest R packages for analyzing affy SNP 6 and 250K as
>>> well as copy number variations for sequencing data? Thanks.
>>
>> The oligo package will do this (although I don't know if it can do the
>> CNV part). You might also look at xps.
>>
>> Best,
>>
>> Jim
>>
>>
>>>
>>> John
>>> [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor@r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>



-- 
Successful people ask better questions, and as a result, they get
better answers. (Tony Robbins)

_______________________________________________
Bioconductor mailing list
Bioconductor@r-project.org
https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
	[[alternative HTML version deleted]]

