[BioC] Erros in crlmm Re: SNP 6 chip

Thu Oct 20 13:50:22 CEST 2011

sorry, please note the typo on my previous email. corrected version below:

if females, use:

crlmm(celFiles, gender=c(2, 2))

b

On 20 October 2011 12:41, Benilton Carvalho <beniltoncarvalho at gmail.com> wrote:
> that not what i meant.
>
> if males, you should run:
>
> crlmm(celFiles, gender=c(1, 1))
>
> if females:
>
> crlmm(celFiles, gender=c(1, 2))
>
> or the combination of the above that holds for your dataset.
>
> b
>
> On 20 October 2011 12:19, John linux-user <johnlinuxuser at yahoo.com> wrote:
>> Hi Benilton
>>
>> Thanks again for your instruction. I set the gender=NULL, and the error
>> still came up. If due to sample size, I will try add another 2 samples,
>> total 4 samples to see if it work. Thanks. J.
>>
>>> system.time(crlmmResult <- crlmm(celFiles, gender=NULL, verbose = FALSE))
>> Welcome togenomewidesnp6Crlmmversion 1.0.4
>>
>> Error: number of cluster centres must lie between 1 and nrow(x)
>> Timing stopped at: 46.67 1.29 47.982
>>>
>>
>>
>> ________________________________
>> From: Benilton Carvalho <beniltoncarvalho at gmail.com>
>> To: John linux-user <johnlinuxuser at yahoo.com>
>> Cc: "Bioconductor at r-project.org" <Bioconductor at r-project.org>
>> Sent: Thursday, October 20, 2011 5:05 AM
>> Subject: Re: Erros in crlmm Re: [BioC] SNP 6 chip
>>
>> Enter manually the gender of the samples through the "gender" argument.
>> You'll also see a warning (not error) saying that it could not do
>> recalibration and that's due to the small sample size.
>> b
>> On Oct 20, 2011 2:45 AM, "John linux-user" <johnlinuxuser at yahoo.com> wrote:
>>
>> 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 at gmail.com>
>> To: cstrato <cstrato at aon.at>
>> Cc: James W. MacDonald <jmacdon at med.umich.edu>; "Bioconductor at r-project.org"
>> <Bioconductor at 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 at 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]]
>>>>>
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>>>
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>>
>>
>>
>> --
>> Successful people ask better questions, and as a result, they get
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>>
>>
>
>
>
> --
> Successful people ask better questions, and as a result, they get
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>

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