Dear Henrik, On May 27, 9:03 pm, Henrik Bengtsson <henrik.bengts...@aroma- project.org> wrote: > On Fri, May 27, 2011 at 4:02 AM, cstratowa > > <christian.strat...@vie.boehringer-ingelheim.com> wrote: > > Dear Henrik, > > > Thank you for this clarification. > > > Since I am still using an older version of aroma.affymetrix which does > > not contain parameter 'lengthRange' I cannot specify the fragment > > length range. > > Just curious, what's the reason for not updating? It's should be a > matter of seconds.
Due to our Firewall settings we have to download all packages manually. Furthermore, we have to install the packages on all of our servers and on the cluster, which I am using to distribute the GLAD jobs. > > > However, at the moment I do not see any disadvantage in > > not specifying lengthRange. When I compare the the CN ranges obtained > > with GLAD between na30 and na31 there are only slight differences due > > to the different annotations. What is your opinion? > > The UGP file that contain genomic positions are probably the same. > > If you are using the FragmentLengthNormalization with the na31 UFLs > provided online, I'm rather sure that you do need to set 'lengthRange' > otherwise you'll get an "identifiability" error, cf. thread 'CRMA v2 > failed at FragmentLengthNormalization for Mouse diversity array' > started on 2011-01-13: > > https://groups.google.com/forum/#!topic/aroma-affymetrix/iRJ7Fggi0JY > > Details on the fragment-lengths in na31 UFL provided online: > > > cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6,Full"); > > ufl <- getAromaUflFile(cdf); > > ufl > > AromaUflFile: > Name: GenomeWideSNP_6 > Tags: Full,na31,hg19,HB20110328 > Full name: GenomeWideSNP_6,Full,na31,hg19,HB20110328 > Pathname: > annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl > File size: 7.18 MB (7526452 bytes) > RAM: 0.00 MB > Number of data rows: 1881415 > File format: v1 > Dimensions: 1881415x2 > Column classes: integer, integer > Number of bytes per column: 2, 2 > Footer: <createdOn>20110328 19:41:33 > PDT</createdOn><platform>Affymetrix</platfo > rm><chipType>GenomeWideSNP_6,Full</chipType><createdBy><fullname>Henrik > Bengtsso > n</fullname><email>[...]</email></createdBy><srcFiles><srcFile1>< > filename>GenomeWideSNP_6,Full.CDF</filename><filesize>493291745</filesize><check > sum>3fbe0f6e7c8a346105238a3f3d10d4ec</checksum></srcFile1><srcFile2><filename>Ge > nomeWideSNP_6.na31.annot.csv</filename><filesize>1501563495</filesize><checksum> > 3f59efe386ffc1af656d01be0ab035e9</checksum></srcFile2><srcFile3><filename>Genome > WideSNP_6.cn.na31.annot.csv</filename><filesize>879257480</filesize><checksum>6a > 21fef62c71fb56bc5dda4499b70a7f</checksum></srcFile3></srcFiles> > Chip type: GenomeWideSNP_6,Full > Platform: Affymetrix > > > summaryOfUnits(ufl) > > snp cnp affxSnp other total > enzyme1-only 577 9609 0 0 10186 > enzyme2-only 502 23432 0 0 23934 > both 929322 912574 0 0 1841896 > missing 1545 211 3022 621 5399 > total 931946 945826 3022 621 1881415 > > The above summary show that there are very few SNPs that exists only > fragments generated by only one of the two enzymes. The estimator of > the fragment-length normalization model requires such SNPs. By > filtering by length using argument 'lengthRange' more and more SNPs > will have a length value on one enzyme only. Although I have updated my package to be able to use CRMAv2, I am still using CRMA for the SNP6.0 arrays, i.e. correcting for allelic cross-talk and for fragment length effects. The reason for this is that I did some testing by comparing CRMAv2 and CRMA for SNP6.0 with real datasets, and the only difference that I saw when looking e.g. at ChromosomeExplorer was that there was a slight decrease in CN values when using CRMAv2. Thus I preferred to stay with CRMA. I am not sure if the fragment length correction for SNP6.0 depends on my choice of using CRMA instead of CRMAv2. In any case not filtering for fragment length does not seem to affect my CN computations. Do you have any comments? Best regards Christian > > Hope this clarifies > > /Henrik > > > > > Best regards > > Christian > > > On May 26, 11:01 pm, Henrik Bengtsson <henrik.bengts...@aroma- > > project.org> wrote: > >> Hi. > > >> On Thu, May 26, 2011 at 4:05 AM, cstratowa > > >> <christian.strat...@vie.boehringer-ingelheim.com> wrote: > >> > Dear Henrik, > > >> > Thank you for the update. > > >> > Meanwhile I have already created the ufl/ugp files by simply modifying > >> > your R-scripts GenomeWideSNP_6,UFL,na30.R and > >> > GenomeWideSNP_6,UGP,na30.R. > > >> > Thus, my question is: Did you do something special or do you still use > >> > these R-scripts? > > >> Nope, nothing special, except that I made sure that the file footer > >> reflects the fact that the date and my initials are correct. > > >> One more thing specific to the na30 -> na31 transition: Affymetrix no > >> longer filter the PCR fragment-length data, which means that the new > >> UFL files now contains fragment lengths of a large range. You now > >> have to specify the range as FragmentLengthNormalization(..., > >> lengthRange=c(400,2000)). > > >> > BTW, on your new web-site I can no longer find these scripts. Are they > >> > still available? > > >> Yes, I did remove the links from the website because it is too much > >> work to also keep those links up-to-date with everything else. > >> Instead, I have added the archive of all build scripts (sorted by chip > >> type and NA revision) to the package itself so that they will be > >> accessible via: > > >> path <- system.file("buildScripts/", package="aroma.affymetrix"); > > >> This will be available in the next release of aroma.affymetrix. Until > >> then, you can also grab/browse them via: > > >>https://r-forge.r-project.org/scm/viewvc.php/pkg/aroma.affymetrix/ins... > > >> As you'll see, that for GenomeWideSNP_6 I am moving towards setting up > >> somewhat interactive user scripts for doing this. You may have to > >> install the R.menu package, i.e. > > >> source("http://aroma-project.org/hbLite.R";); > >> hbLite("R.menu"); > > >> Hope this helps > > >> Henrik > > >> > Best regards > >> > Christian > > >> > On May 26, 3:36 am, Henrik Bengtsson <henrik.bengts...@aroma- > >> > project.org> wrote: > >> >> A late follow up/to close this thread: > > >> >> The requested na31/hg19 annotation files are now available: > > >> >>http://aroma-project.org/chipTypes/GenomeWideSNP_6 > > >> >> /Henrik > > >> >> On Mon, Mar 28, 2011 at 6:48 AM, cstratowa > > >> >> <christian.strat...@vie.boehringer-ingelheim.com> wrote: > >> >> > Dear Henrik, > > >> >> > I am also looking for the new (old) na31 annotation files for SNP6. > > >> >> > I have seen that for the Nsp/Sty arrays you have put the na31 (hg19) > >> >> > ufl/ugp files on the Chip types web-site for download. > > >> >> > However, the web-site for SNP6 still contains the old na30 (hg18) ufl/ > >> >> > ugp files. > >> >> > Is it possible to update this site to the new na31 (hg19) ufl/ugp > >> >> > files, too? > > >> >> > Best regards > >> >> > Christian > > >> >> > On Feb 2, 9:39 am, Mete Civelek <mete.cive...@gmail.com> wrote: > >> >> >> Hi All, > > >> >> >> A few weeks ago there was a discussion about ugp and ufl files based > >> >> >> on the hg19 annotation. Are those files available for share? > > >> >> >> Thank you > > >> >> > -- > >> >> > 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 > >> >> > websitehttp://www.aroma-project.org/. > >> >> > To post to this group, send email to aroma-affymetrix@googlegroups.com > >> >> > To unsubscribe and other options, go > >> >> > tohttp://www.aroma-project.org/forum/ > > >> > -- > >> > 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 > >> > websitehttp://www.aroma-project.org/. > >> > To post to this group, send email to aroma-affymetrix@googlegroups.com > >> > To unsubscribe and other options, go > >> > tohttp://www.aroma-project.org/forum/ > > > -- > > 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 websitehttp://www.aroma-project.org/. > > To post to this group, send email to aroma-affymetrix@googlegroups.com > > To unsubscribe and other options, go tohttp://www.aroma-project.org/forum/ -- 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-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
