[BioC] crlmm warning

Benilton Carvalho bcarvalh at jhsph.edu
Thu Mar 8 22:35:06 CET 2007 

if you want the matrix with the genotype calls:

calls(crlmm_NSP)

if you want the matrix with the confidence associated to each call:

callsConfidence(crlmm_NSP)

does that help?

b

On Mar 8, 2007, at 4:30 PM, morten mattingsdal wrote:

> Hi again,
>
> Nice ! Now crlmm finishes with no errors and I can hardly wait to  
> do linkage analysis on the results. But I'm afraid I have one final  
> question for you.
> How to export the data to a txt file? Im used to work with exprSet  
> objects, and I took a shot at converting the results from crlmm  
> using the code (with works for ordinary rma, gcrma and expresso  
> "returns"):
>
>> out_NSP=as.matrix(exprs(crlmm_NSP))
>> Error in function (classes, fdef, mtable)  :
>>        unable to find an inherited method for function "exprs",  
>> for signature "SnpCallSet"
>> Error in as.matrix(exprs(crlmm_NSP)) : error in evaluating the  
>> argument 'x' in selecting a method for function 'as.matrix'
>
> Ideally I want a matrix with columns corresponding to arrays and  
> rows corresponding to individual probe ID.
>
> Is this possible ?
>
> best
> morten
>
>
>
>> Hi Morten,
>>
>> I'm writing a vignette to help users with oligo. My bad! Sorry for  
>> that.
>>
>> All you need to do is give a file name... if the file does not exist,
>> it'll be created... if it exists, it'll be loaded.
>>
>> For example, try the following:
>>
>> crlmm_NSP=crlmm(rma_NSP, correctionFile="nspCorrection.rda")
>>
>> The reason this is required (at least for now) is because the EM
>> algorithm may take a long time depending on the sample size. So, once
>> it is done, it saves the results in this correctionFile... which you
>> can just load later in case you want to run CRLMM again.
>>
>> If for some reason you need to run CRLMM on the exact same data
>> (rma_NSP), by using
>>
>> crlmm_NSP=crlmm(rma_NSP, correctionFile="nspCorrection.rda")
>>
>> the EM step will be skipped and loaded from nspCorrection.rda  
>> instead.
>>
>> b
>>
>> On Mar 7, 2007, at 9:55 AM, Morten Mattingsdal wrote:
>>
>>> Hi Benilton,
>>>
>>> Readning the data, loading annotation libraries and rma
>>> normalizting goes perfect!
>>> But I encounter an error in crlmm, which will probably expose my
>>> ignorance here, but crlmm complains about a "correctionFile is not
>>> found".
>>>
>>>> crlmm_NSP=crlmm(rma_NSP)
>>>> Error in crlmm(rma_NSP) : Provide correctionFile.
>>>> If the correctionFile is not found, it will be created and it will
>>> contain the EM results.
>>>
>>> The error claims, if not found it will be created. I don't think it
>>> is created, although I have an R object called "reference"
>>>
>>> The crlmm doc says: The 'correction' argument is a list with the
>>> following elements:
>>> 'f0' (scalar), 'fs' (numeric vector), 'pis' (numeric matrix) and
>>> 'snr'.
>>>
>>> I cant seem to figure out the nature of these correction elements
>>> nor the data format of this file.
>>> Could you be so kind and explain a bit what this means ?
>>>
>>> regards
>>> morten
>>>
>>>
>>> NB Ill just paste all commands and output for your leisure
>>>
>>>> library(oligo)
>>>
>>>> files <- list.celfiles()
>>>
>>>> files()
>>> [1] "1580_Nsp1_090207.CEL" "1620_Nsp1_020307.CEL"
>>> "1736_Nsp1_020307.CEL"
>>> [4] "1812_Nsp1_020307.CEL" "355_Nsp1_090207.CEL"
>>> "4379_Nsp1_020307.CEL"
>>> [7] "4436_Nsp1_020307.CEL" "5968_Nsp1_020307.CEL"
>>> "635_Nsp1_090207.CEL"
>>> [10] "654_Nsp1_090207.CEL"  "659_Nsp1_090207.CEL"
>>> "680_Nsp1_090207.CEL"
>>>
>>>> NSP <- read.celfiles(files)
>>> Incompatible phenoData object. Created a new one.
>>>
>>>
>>> Welcome to the pd.Mapping250K_Nsp prototype pdInfo package
>>> WARNING: DO NOT USE THIS PACKAGE FOR ANY ANALYSIS.
>>> THIS PACKAGE IS FOR INTERFACE PROTOTYPE USE ONLY!
>>> THE DATA HAS NOT BEEN VALIDATED AND LIKELY HAS ERRORS.
>>> Have fun!
>>>
>>> Platform design info loaded.
>>>
>>>> rma_NSP <- snprma(NSP)
>>> Position  -4
>>> Position  -2
>>> Position  -1
>>> Position  0
>>> Position  1
>>> Position  3
>>> Position  4
>>> Loading required package: pd.mapping250k.nsp.crlmm.regions
>>> Calculating Expression
>>>
>>>> crlmm_NSP=crlmm(rma_NSP)
>>> Error in crlmm(rma_NSP) : Provide correctionFile.
>>> If the correctionFile is not found, it will be created and it will
>>> contain the EM results.
>>>
>>>
>>>> sessionInfo()
>>> R version 2.5.0 Under development (unstable) (2007-03-04 r40813)
>>> x86_64-unknown-linux-gnu
>>>
>>> locale:
>>> LC_CTYPE=no_NO;LC_NUMERIC=C;LC_TIME=C;LC_COLLATE=C;LC_MONETARY=C;LC_ 
>>> ME
>>> SSAGES=C;LC_PAPER=C;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASURE 
>>> ME
>>> NT=C;LC_IDENTIFICATION=C
>>>
>>> attached base packages:
>>> [1] "splines"   "tools"     "stats"     "graphics"  "grDevices"
>>> "utils"   [7] "datasets"  "methods"   "base"
>>> other attached packages:
>>> pd.mapping250k.nsp.crlmm.regions               pd.mapping250k.nsp
>>>                         "0.1.0"                          "0.1.5"
>>>                     geneplotter                          lattice
>>>                        "1.13.7"                        "0.14-16"
>>>                        annotate                            oligo
>>>                        "1.13.6"                        "0.99.82"
>>>           BufferedMatrixMethods                   BufferedMatrix
>>>                         "0.1.1"                         "0.1.27"
>>>                         RSQLite                              DBI
>>>                        "0.4-20"                         "0.1-12"
>>>                          affyio                          Biobase
>>>                         "1.3.3"                        "1.13.39"
>>>
>>> Benilton Carvalho wrote:
>>>> Hi Morten,
>>>>
>>>> the 'safe' versions will become available with BioC 2.0.
>>>>
>>>> My question, regarding the email you send next (about using
>>>> makePlatformDesign for SNP arrays), that's not required anymore.
>>>> All you need is in that oligoAddOns.tar.gz. All you need to do is
>>>> install the packages and use the latest oligo.
>>>>
>>>> Let me know how things go,
>>>>
>>>> b
>>>>
>>>> On Mar 7, 2007, at 5:45 AM, Morten Mattingsdal wrote:
>>>>
>>>>> Hello everyone,
>>>>>
>>>>> Ive managed to get the oligo package and the crlmm function up and
>>>>> running. Ive also installed the meta-data libraries from this URL
>>>>> http://www.biostat.jhsph.edu/~bcarvalh/oligoAddOns.tar.gz
>>>>> provided by Benliton
>>>>>
>>>>> but when I run the commands:
>>>>>
>>>>>> files <- list.celfiles()
>>>>>> snpFSet <- read.celfiles(files)
>>>>>>
>>>>>> Welcome to the pd.Mapping250K_Nsp prototype pdInfo package
>>>>>> WARNING: DO NOT USE THIS PACKAGE FOR ANY ANALYSIS.
>>>>>> THIS PACKAGE IS FOR INTERFACE PROTOTYPE USE ONLY!
>>>>>> THE DATA HAS NOT BEEN VALIDATED AND LIKELY HAS ERRORS.
>>>>>> Have fun!
>>>>>
>>>>> Im am happy that this information is warning me, but to my point:
>>>>> - When will the "safe" mapping libraries come?
>>>>> - Can I build this by myself ?
>>>>>
>>>>> I want to compare brlmm from Affymetrix and crlmm from BioC  
>>>>> genotype
>>>>> calls for my data
>>>>>
>>>>> regards
>>>>> morten
>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor at stat.math.ethz.ch
>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>> Search the archives: http://news.gmane.org/
>>>>> gmane.science.biology.informatics.conductor
>>>>
>>>>
>>>> .
>>>>
>
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