[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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