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. > 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. /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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