[BioC] crlmm warning
Benilton Carvalho
bcarvalh at jhsph.edu
Wed Mar 7 17:16:31 CET 2007
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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>>
>>
>> .
>>
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