Hi Carles,
the quick answer it that aroma.affymetrix only implements the CRLMM
method for the 100K (Mapping50K_Xba142 and Mapping50K_Hind142) and
500K (Mapping250K_Nsp and Mapping250K_Sty) chip types. For newer
methods you need to turn to the Bioconductor 'oligo' package.
However, what are you going to use the genotypes for? I'm asking
because it is rather common, and according to me incorrect, to try to
call genotypes in tumor samples. Genotypes are really only defined in
normal/germline genomes and most (all?) genotype methods assume that
the samples are such. Calling "genotypes" in tumors is rather a
problem of inferring parent-specific CNs (PSCNs) - not at the
SNP-by-SNP level but in segments along the genome. Contrary to normal
PSCNs ("genotypes"), tumor PSCNs may not take discrete levels due
clonality and normal contamination. In other words, if you do indeed
have tumors, it does not make sense to use CRLMM on them. Instead you
want to to PSCN segmentation/calling.
Hope this helps
Henrik
On Fri, Mar 22, 2013 at 7:47 AM, Carles Hernández <kuragari...@gmail.com> wrote:
> Good afternoon,
>
> I am trying to analyse a set of CEL files from Affymetrix GenomeWideSNP 6.0
> and get its LRR, FreqB and genotype (for all individuals and for all
> chromosomes).
>
> I have started with the vignettes "CRMA (v1): Total copy number analysis
> using CRMA v1 (10K, 100K, 500K)" and "CRMA (v2): Estimation of total copy
> numbers using the CRMA v2 method (10K-CytoScanHD)" since I am new in this
> world of microarrays analysis.
>
> But I didn't fine any way to retrieve the genotype I moved to "CRLMM
> genotyping (100K and 500K)".
>
> So, from both methods I can get the LRR and FreqB with extactCNT of with
> extractTotalAndFraqB but only from the second one (CRLMM) I can use the
> extractGenotypes (becouse the chiptype's crlmm model is required). On the
> other hand when I try to create the crlmm model for GenomeWideSNP 6.0 the
> following error succeed:
>
>
> Exception: Cannot fit CRLMM model: Model fitting for this chip type is not
> supported/implemented: GenomeWideSNP_6
> at #02. CrlmmModel(ces, tags = "*,oligo")
> - CrlmmModel() is in environment 'aroma.affymetrix'
> at #01. process_dataset("GenomeWideSNP_6", "gal", verbose = TRUE)
> - process_dataset() is in environment 'R_GlobalEnv'
> Error: Cannot fit CRLMM model: Model fitting for this chip type is not
> supported/implemented: GenomeWideSNP_6
>
>
> So... Am I doing something wrong? If no, is there some way to get the full
> set of data I need (sample's name, sample's position, chromosome, LRR, FraqB
> and genotype) using a single method?
>
> My full code-snippet:
>
> library( 'aroma.affymetrix' )
>
>
> write_table <- function( dataset, file_name ) {
> [...]
> }
>
> process_dataset <- function( dataset_name chip_type ) {
> cdf <- AffymetrixCdfFile$byChipType( chip_type );
> csR <- AffymetrixCelSet$byName( dataset_name, cdf=cdf );
> ces <- justSNPRMA( csR, normalizeToHapmap=TRUE, returnESet=FALSE );
> crlmm <- CrlmmModel( ces, tags="*,oligo" );
> units <- fit( crlmm, ram="oligo" );
> callSet <- getCallSet( crlmm );
>
>
> gi <- getGenomeInformation( cdf );
>
>
> for( array in 1:length( csR ) ) {
> ds <- NULL;
> ce <- getFile( ces, array );
> for( chr in chr_list ) {
> chrunits <- getUnitsOnChromosome( gi, chromosome=chr );
> chrnames <- getUnitNames( cdf, units=chrunits )
> pos <- getPositions( gi, units=chrunits ); # / 1e6;
> cf <- getFile( callSet, array );
> calls <- extractGenotypes( cf, units=chrunits );
> dta <- extractTotalAndFreqB( ce, units=chrunits );
> theta <- dta[,"total"];
>
> ceR <- getAverageFile( ces );
> dataR <- extractTotalAndFreqB( ceR, units=chrunits );
> thetaR <- dataR[,"total"];
>
> l2r <- log2(theta/thetaR);
> ds <- add_to_ds( chrnames, rep( chr, length( chrnames ) ),
> pos, l2r, dta[,"FreqB"], calls );
> }
> colnames( ds ) <- c( "Name", "Chr", "Position", "Log.R.Ratio",
> "B.Allele.Freq", "GType" );
> write_table( ds, paste0( getName( ce ), ".txt" ) )
> }
> }
> }
>
> process_dataset( "GenomeWideSNP_6", "gal" )
>
> --
> --
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