[BioC] crlmm warning

morten mattingsdal mortenm at inbox.com
Thu Mar 8 22:30:11 CET 2007 

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_MEASUREME
>> 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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>>>> Bioconductor at stat.math.ethz.ch
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>>> 
>>> 
>>> .
>>>

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