[BioC] crlmm warning

[Morten Mattingsdal]

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_MESSAGES=C;LC_PAPER=C;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=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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>
>
> .
>