Hi. On Thu, Oct 2, 2008 at 2:39 AM, marco <[EMAIL PROTECTED]> wrote: > > Dear Henrik, > > I tried the X chromosome variant but I am not sure I can het it to > work. > I made a *.saf file and place it into annotationData/samples/ > File looks like this: > > name:MD10 > tags:XY > name:MD11 > tags:XY > name:MD12 > tags:XY > name:MD13 > ... > ...
This looks correct to me. Maybe you should try to add an empty line between the entries. What is the full filename of this file? > > Anyway I cannot get the function getAttributes to work, so I am unsure > if the *.saf is read correctly. > Below is the output: >> cdf <- AffymetrixCdfFile$fromChipType("GenomeWideSNP_6", tags="Full") >> print(cdf) > AffymetrixCdfFile: > Path: annotationData/chipTypes/GenomeWideSNP_6 > Filename: GenomeWideSNP_6,Full.cdf > Filesize: 470.44MB > Chip type: GenomeWideSNP_6,Full > RAM: 0.00MB > File format: v4 (binary; XDA) > Dimension: 2572x2680 > Number of cells: 6892960 > Number of units: 1881415 > Cells per unit: 3.66 > Number of QC units: 4 >> gi <- getGenomeInformation(cdf) >> print(gi) > UgpGenomeInformation: > Name: GenomeWideSNP_6 > Tags: Full,na24,HB20080214 > Pathname: annotationData/chipTypes/GenomeWideSNP_6/ > GenomeWideSNP_6,Full,na24,HB20080214.ugp > File size: 8.97MB > RAM: 0.00MB > Chip type: GenomeWideSNP_6,Full >> si <- getSnpInformation(cdf) >> print(si) > UflSnpInformation: > Name: GenomeWideSNP_6 > Tags: Full,na24,HB20080214 > Pathname: annotationData/chipTypes/GenomeWideSNP_6/ > GenomeWideSNP_6,Full,na24,HB20080214.ufl > File size: 7.18MB > RAM: 0.00MB > Chip type: GenomeWideSNP_6,Full > Number of enzymes: 2 >> cs <- AffymetrixCelSet$fromName("ESC", cdf=cdf) If you do cs <- AffymetrixCelSet$fromName("ESC", cdf=cdf, verbose=-20) You should see from the output showing what SAF files are located and that they are read, e.g. cdf <- AffymetrixCdfFile$byChipType("Mapping50K_Hind240"); csR <- AffymetrixCelSet$byName("HapMap270,100K,CEU,testSet", cdf=cdf, verbose=-20); ... 20081004 16:47:49| Allocating a new AffymetrixCelSet instance...done 20081004 16:47:49| Updating newly allocated AffymetrixCelSet... 20081004 16:47:49| Updating AffymetrixCelSet... 20081004 16:47:49| Scanning for and applying sample annotation files... SampleAnnotationSet: Name: annotationData Tags: Full name: annotationData Number of files: 7 Names: 000.default, AGRF_2007a, ..., HapMap270 Path (to the first file): annotationData/samples Total file size: 0.03MB RAM: 0.00MB 20081004 16:47:50| Scanning for and applying sample annotation files...done 20081004 16:47:50| Updating AffymetrixCelSet...done 20081004 16:47:50| Updating newly allocated AffymetrixCelSet...done 20081004 16:47:50| Defining an AffymetrixCelSet object from files...done ... >> print(cs) > AffymetrixCelSet: > Name: ESC > Tags: > Path: rawData/ESC/GenomeWideSNP_6 > Platform: Affymetrix > Chip type: GenomeWideSNP_6,Full > Number of arrays: 26 > Names: MD10, MD11, ..., VT06_TER2102EP > Time period: 2008-07-11 11:09:02 -- 2008-09-03 14:47:43 > Total file size: 1712.75MB > RAM: 0.04MB >> cf <- getFile(cs, indexOf(cs, "MD10")); > AffymetrixCelFile: > Name: MD10 > Tags: > Pathname: rawData/ESC/GenomeWideSNP_6/MD10.CEL > File size: 65.88MB > RAM: 0.01MB > File format: v1 (binary; CC) > Platform: Affymetrix > Chip type: GenomeWideSNP_6,Full > Timestamp: 2008-07-17 19:31:03 >> attrs <- getAttributes(cf); > Error in order(names(attrs)) : argument 1 is not a vector This does indeed indicate that there were no attributes set, i.e. it looks like the *.saf file was not located. (In next release, this will return NULL instead of giving an error). Did the above help? /Henrik >> sessionInfo() > > R version 2.7.2 (2008-08-25) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices datasets utils methods > base > > other attached packages: > [1] aroma.affymetrix_0.9.4 aroma.apd_0.1.3 > R.huge_0.1.6 > [4] affxparser_1.12.2 aroma.core_0.9.4 > sfit_0.1.5 > [7] aroma.light_1.8.1 digest_0.3.1 > matrixStats_0.1.3 > [10] R.rsp_0.3.4 R.cache_0.1.7 > R.utils_1.0.4 > [13] R.oo_1.4.6 R.methodsS3_1.0.3 > > > Best Regards > > Marco > > > > > > > On Sep 19, 10:10 pm, "Henrik Bengtsson" <[EMAIL PROTECTED]> > wrote: >> Hi. >> >> On Fri, Sep 19, 2008 at 4:35 AM, marco <[EMAIL PROTECTED]> wrote: >> >> > Dear List, >> >> > I wonder about how X chromosome is treated in aroma.affymetrix. >> > Is the mix of male/female samples somehow taken into account, or X is >> > processed as any other chromosome? >> >> Good idea ;) Yes, the CRMA model does take into account the fact >> that different samples have different ploidies on ChrX when using the >> pool of arrays as a reference. The idea is to calculate the robust >> average across all arrays and correct for the bias that >> non-copy-neutral samples introduce. See Section '3.2.7 Reference >> signals' in: >> >> H. Bengtsson; R. Irizarry; B. Carvalho; T. Speed, Estimation and >> assessment of raw copy numbers at the single locus level, >> Bioinformatics, 2008. [pmid: 18204055] [doi: >> 10.1093/bioinformatics/btn016] >> >> for more details. The model/method requires that at least one sample >> is copy neutral, i.e. you need at least one "female" in order to >> estimate a diploid reference on ChrX. The same bias-correction >> method can also be used when some of samples are say trisomy 21. For >> ChrY, our current model cannot give you a *diploid* ChrY reference, >> but a *copy neutral* one, i.e. CN=1 (requires at least one "male"). >> To the best of my understand, none of the other methods out there use >> this, but instead it is common to see that only female samples are >> used for the ChrX reference. See the above CRMA paper to see how much >> the ChrX CN estimates are improved when you use the above >> bias-corrected method instead. >> >> >> >> > In these case the female and males test array are supposed to have >> > log2 values on the average over and below zero? >> >> I'm note sure what you mean by this, but maybe the above answered this >> question too. >> >> So, how do you do this in aroma.affymetrix? I have on purpose avoided >> giving the details on this until someone asks for it, because it >> involved the use of a new kind of non-finalized sample annotation >> files (SAFs). I don't want to bother people with alpha versions in >> case the API/format changes. It is unlikely that it will change much >> but if you can accept that it might change, I created a new vignette >> explaining how to do it: >> >> Vignette 'Sex-chromosome bias-corrected reference signals from pooled >> average'http://groups.google.com/group/aroma-affymetrix/web/sex-chromosome-bi... >> >> It also illustrated a lot of other things so it might be useful for others >> too. >> >> Hope this helps >> >> Henrik >> >> >> >> > Regards >> >> > Marco > > > --~--~---------~--~----~------------~-------~--~----~ 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. 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