[BioC] crlmm warning

morten mattingsdal mortenm at inbox.com
Thu Mar 8 22:39:01 CET 2007 

It works perfectly !
thanks
morten


> 
> 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
>>>>>> 
>>>>>> _______________________________________________
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>>>>> 
>>>>> 
>>>>> .
>>>>> 
>> 
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