Good afternoon, First of all offer my apologies for the delay of this response.
El sábado, 23 de marzo de 2013 22:28:52 UTC+1, Henrik Bengtsson escribió: > > Hi. > > On Sat, Mar 23, 2013 at 4:00 AM, Carles Hernández > <kurag...@gmail.com<javascript:>> > wrote: > > Good morning, > > > > First of all, thanks for answering so fast. Its really helpful to be > able to > > talk with the main creator of the library. > > > > Going back to the topic, sorry I didn't express myself properly. I "have > no > > idea" what the CEL files contain so, the idea is to analyze the > microarrays > > using, the FreqB, LRR and genotypes. Some of them can are tumoral but I > > can't know. I will use the genotype to classify the probes in AA, Ab and > BB > > in order to study the FreqB compared with LRR and use an external > program > > called MAD. > > But do you agree with me that it does not make sense to classify a SNP > into (AA, AB, BB), i.e. call the genotype, if the SNP is for instance > A, ABB, AAABB, or even worse a mixture of, say, 10% A, 38.5% ABB and > 40.1% AAABB and the rest being the normal AB? So, I still argue that > genotypes will only make sense for SNPs that you know are normal. If > you don't know which samples are normal and which are tumors you will > never know which SNPs/genotype calls you can trust, which to me makes > the (artifical) genotype calls useless. Although I still haven't seen > one, I'm all ear for a good argument for where it makes sense to call > genotypes in a tumor. I'm just trying to safe you from wasting your > time going down the wrong path. > Yes, I agree with that but in fact I want a baf estimation and for that I want to use CRLMM, which also predicts the genotype, but it is not ready for GenomeWideSNP 6 so use the implementation of CRMAv2 which predicts baf pretty well it may be a solution. Could you provide a reference to "MAD" - never heard of it. > Here you can get some information related to "MAD": - http://www.biomedcentral.com/1471-2105/12/166 - http://www.creal.cat/jrgonzalez/software.htm#ancla-MAD > > > So, you said CRLMM is not implemented for GenomeWideSNP 6.0, may I can > > contribute implementing it? > > Certainly, that would be great and most appreciated. Just a heads up, > it's more than a standard programming task. It requires diving into > the oligo::crlmm() code and its algorithm to find out which modules > can be reused and which needs to be ported. The two CrlmmModel.R and > CrlmmModel.EXT.R in aroma.affymetrix/R/ would serve as a good > start/template: > > > https://r-forge.r-project.org/scm/viewvc.php/pkg/aroma.affymetrix/R/CrlmmModel.R?view=markup&root=aroma-dots > > > https://r-forge.r-project.org/scm/viewvc.php/pkg/aroma.affymetrix/R/CrlmmModel.EXT.R?view=markup&root=aroma-dots > > > If you look inside oligo::crlmm() you see that it itself takes two > separate paths depending whether the chip type is (a) > Mapping50K_(Hind|Xba)240 and Mapping250K_(Nsp|Sty) [which is ported to > aroma.affymetrix], or (b) GenomeWideSNP_(5|6) [which is not ported]. > In other words, it's the internal oligo:::genotypeOne() that needs to > be ported. > Actually I am battling with clrmm, oligo and oligoClasses to manage my GenomeWideSNP cel files. My prior is to finish this analysis but may be I will take a hand on this porting, not sure but in mind. > > > > Anyway, thank you to share with us the aroma.affymetrix suite. > > You're welcome - hopefully it makes everyday science a bit easier. > > /Henrik > Lots of thanks for you answers. Carles PS\ Some consideration to apply CRLMM to Affymetrix Axiom and Affymetrix Axiom Exome arrays? > > > > > > El viernes, 22 de marzo de 2013 19:31:10 UTC+1, Henrik Bengtsson > escribió: > >> > >> 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 <kurag...@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" ) > >> > > >> > -- > >> > -- > >> > When reporting problems on aroma.affymetrix, make sure 1) to run the > >> > latest > >> > version of the package, 2) to report the output of sessionInfo() and > >> > traceback(), and 3) to post a complete code example. > >> > > >> > > >> > You received this message because you are subscribed to the Google > >> > Groups > >> > "aroma.affymetrix" group with website http://www.aroma-project.org/. > >> > To post to this group, send email to aroma-af...@googlegroups.com > >> > To unsubscribe and other options, go to > >> > http://www.aroma-project.org/forum/ > >> > > >> > --- > >> > You received this message because you are subscribed to the Google > >> > Groups > >> > "aroma.affymetrix" group. > >> > To unsubscribe from this group and stop receiving emails from it, > send > >> > an > >> > email to aroma-affymetr...@googlegroups.com. > >> > For more options, visit https://groups.google.com/groups/opt_out. > >> > > >> > > > > > -- > > -- > > When reporting problems on aroma.affymetrix, make sure 1) to run the > latest > > version of the package, 2) to report the output of sessionInfo() and > > traceback(), and 3) to post a complete code example. > > > > > > You received this message because you are subscribed to the Google > Groups > > "aroma.affymetrix" group with website http://www.aroma-project.org/. > > To post to this group, send email to > > aroma-af...@googlegroups.com<javascript:> > > To unsubscribe and other options, go to > http://www.aroma-project.org/forum/ > > > > --- > > You received this message because you are subscribed to the Google > Groups > > "aroma.affymetrix" group. > > To unsubscribe from this group and stop receiving emails from it, send > an > > email to aroma-affymetr...@googlegroups.com <javascript:>. > > For more options, visit https://groups.google.com/groups/opt_out. > > > > > -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. 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