On Tue, Sep 28, 2010 at 12:03 PM, hb <h...@biostat.ucsf.edu> wrote: > Hi. > > On Tue, Sep 28, 2010 at 11:54 AM, Patrick Danaher <patrickjdana...@gmail.com> > wrote: >> Hi Henrik, >> Thanks for your response. The thread you suggested ( http://goo.gl/FGVe ) >> describes my problem well - I'm getting a very similar intensity profile for >> some chromosomes in some samples. The attached png shows the problem (red >> dots are intensities; the black dots are from a copy number calling problem >> and can be ignored). The second figure plots the called intensities against >> normal reference intensities for the same loci. >> As for your specific questions: I've never used CRMAv2 before, my dataset >> isn't public, and it's an affy 6.0 chip. > > What's your chip type? The other thread reported problems on Mapping250K_Sty > though labelled as "Sty 2" and I don't know what the "2" means there.
Woops, I read it as it was *not* a GenomeWideSNP_6 chip in your "...and it's an affy 6.0 chip" note. So, it is GenomeWideSNP_6. > >> Do you think annotation issues would cause this problem only in a small >> subset of my samples? > > When I say annotation issues, I really mean that if the CDF for the chip type > is not the correct one, you might pick up the wrong probe signals, especially > for SNPs, e.g. PM_A may get the value of a total CN probe once in a while, > say. It could be a software/annotation bug in the Affymetrix DAT to CEL file > conversion and so on. That's why it is crucial to know more about the chip > used. > > I also recommend that you try dChip and/or Affymetrix GTC, if possible. Since it is GenomeWideSNP_6, you should be able to try it on Affymetrix GTC. /Henrik > > /Henrik > >> Thanks, >> Patrick >> On Sun, Sep 26, 2010 at 1:36 PM, Henrik Bengtsson <h...@aroma-project.org> >> wrote: >>> >>> Hi. >>> >>> On Mon, Sep 13, 2010 at 4:19 PM, Patrick <patrickjdana...@gmail.com> >>> wrote: >>> > Hi everyone, >>> > I'm using AROMA's implementation of the CRMA v2 method to get copy >>> > number estimates for cancer samples, and I'm getting a very unusual >>> > result. Many of the samples have a chromosome where AROMA has called >>> > primarily copy number gains or losses, and the losses are mixed in >>> > with each other. That is, if you plot the probes' intensities by >>> > their positions on the chromosome, you see large stretches (~10,000 >>> > probes) where there are no intensities in the normal range >>> > (corresponding to no gain or loss), and there are intensities both >>> > above and below the normal range, mixed in with each other along the >>> > chromosome. It is as if the plots for a chromosome with a long >>> > deletion and a chromosome with a long addition were laid atop each >>> > other. >>> >>> It is not 100% clear from your description what you are observing. >>> Note that it is possible to attach PNGs to messages sent to this >>> mailing list as long as you send it as an email (not via the web >>> interface). What chip type are you working on and do you look at a >>> public data set? Have you used CRMAv2 on other data sets without a >>> problem? >>> >>> FYI, Johan Staaf reported odd looking copy number results that are >>> reproducible and very odd. See thread 'Problems with Affymetrix 250K >>> Sty2 arrays after CRMAv2 analysis' on June 23-August 5, 2010, cf. >>> http://goo.gl/FGVe. From the discussion in that thread, it seems to >>> have something to do with annotation issues, but it is still to be >>> solved. Is that what you are experiencing? >>> >>> > It seems implausible that a cancer sample would have copy number gains >>> > and losses mixed in with each other in such small intervals, over such >>> > large stretches of chromosome, without any loci having the usual 2 >>> > copies, so I suspect the normalization or the affy array is the source >>> > of this phenomenon. I looked at the data without using AROMA, and the >>> > phenomenon was not evident. I re-normalized the data 3 times, each >>> > time using only one step of the AROMA normalization in isolation. The >>> > base position normalization step produced the phenomenon, and the >>> > allele crosstalk calibration and the fragment length normalization >>> > steps did not. >>> >>> What would help troubleshooting is if you could see other software >>> such as dChip of Affymetrix GTC produces the same oddities. If they >>> do, we know for sure it's something odd with the annotation. >>> >>> /Henrik >>> >>> > Any thoughts on what I'm seeing and on how the base pair normalization >>> > could cause it would be very appreciated. >>> > Thanks, >>> > Patrick >>> > >>> > -- >>> > 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/ >>> > >>> >>> -- >>> 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/ >> >> -- >> 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/ >> > > -- 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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