QC Affy 6.0 SNP arrays with crlmm or Oligo?

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jeremy wilson ▴ 150

@jeremy-wilson-3700

Last seen 10.2 years ago

Dear all, I am wondering if there is a QC methodology like the "contrast QC" check by the affymetrix genome console to QC the arrays before genotyping. The crlmm and Oligo packages do the normalization and summarization which is awesome but I do not see it doing QC checks. I am trying to see the quality of the chips with nice plots similar to that of from "arrayQualityMetrics" package for gene expression arrays. One more question: I have only 8 arrays from the same lab and I need to do LOH and copy number analysis. Will the small number of arrays be problematic? Awaiting for your reply, Thank you JW

Normalization oligo crlmm Normalization oligo crlmm • 1.7k views

ADD COMMENT • link updated 14.7 years ago by Benilton Carvalho ★ 4.3k • written 14.7 years ago by jeremy wilson ▴ 150

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Benilton Carvalho ★ 4.3k

@benilton-carvalho-1375

Last seen 4.7 years ago

Brazil/Campinas/UNICAMP

Hi Jeremy, currently there isn't anything like arrayQualityMetrics implemented in oligo/crlmm. About the sample size, you need at least 10 samples to use crlmm::computeCopynumber. b On Wed, Mar 17, 2010 at 4:45 PM, jeremy wilson <jeremy.wilson88 at="" gmail.com=""> wrote: > Dear all, > > I am wondering if there is a QC methodology like the "contrast QC" > check by the affymetrix genome console to QC the arrays before > genotyping. The crlmm and Oligo packages do the normalization and > summarization which is awesome but I do not see it doing QC checks. I > am trying to see the quality of the chips with nice plots similar to > that of from "arrayQualityMetrics" package for gene expression arrays. > > One more question: I have only 8 arrays from the same lab and I need > to do LOH and copy number analysis. Will the small number of arrays be > problematic? > > Awaiting for your reply, > Thank you > JW > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >

ADD COMMENT • link 14.7 years ago Benilton Carvalho ★ 4.3k

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Thanks for the reply dear Benilton.. how can then one proceed with QC'ing SNP arrays using BioC? Considering the quality of arrays are good, does the crlmm algorithm give good call rates with higher accuracy compared to the Birdseed algorithm from Affy genome console and the BirdSuit from Broad MIT? I read in one of your papers (http://biostatistics.oxfordjournals.org/cgi/content/full/8/2/485) that the crlmm outperforms other competing algorithms. In the article, was the crlmm alg compared to DM alg or Birdseed? Does crlmm perform better even now when compared to the Birdseed? In my case, how should I do the CNV analysis with only 8 samples. Are there any other packages or adjustments you can suggest me to compensate for the small sample size? Please let me know Thank you On Wed, Mar 17, 2010 at 12:17 PM, Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> wrote: > Hi Jeremy, > > currently there isn't anything like arrayQualityMetrics implemented in > oligo/crlmm. > > About the sample size, you need at least 10 samples to use > crlmm::computeCopynumber. > > b > > On Wed, Mar 17, 2010 at 4:45 PM, jeremy wilson > <jeremy.wilson88 at="" gmail.com=""> wrote: >> Dear all, >> >> I am wondering if there is a QC methodology like the "contrast QC" >> check by the affymetrix genome console to QC the arrays before >> genotyping. The crlmm and Oligo packages do the normalization and >> summarization which is awesome but I do not see it doing QC checks. I >> am trying to see the quality of the chips with nice plots similar to >> that of from "arrayQualityMetrics" package for gene expression arrays. >> >> One more question: I have only 8 arrays from the same lab and I need >> to do LOH and copy number analysis. Will the small number of arrays be >> problematic? >> >> Awaiting for your reply, >> Thank you >> JW >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >

ADD REPLY • link 14.7 years ago jeremy wilson ▴ 150

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Hi Jeremy, you may want to take a look at: http://www.ncbi.nlm.nih.gov/pubmed/19906825 http://www.ncbi.nlm.nih.gov/pubmed/18387188 in summary, crlmm has been compared to BRLMM, BRLMM-P and, more recently, to Birdseed. Regarding CNV, we currently don't have anything implemented for small samples in oligo/crlmm. But Henrik already gave you some suggestions... ;) b On Wed, Mar 17, 2010 at 8:45 PM, jeremy wilson <jeremy.wilson88 at="" gmail.com=""> wrote: > Thanks for the reply dear Benilton.. > > how can then one proceed with QC'ing SNP arrays using BioC? > > Considering the quality of arrays are good, does the crlmm algorithm > give good call rates with higher accuracy compared to the Birdseed > algorithm from Affy genome console and the BirdSuit from Broad MIT? I > read in one of your papers > (http://biostatistics.oxfordjournals.org/cgi/content/full/8/2/485) > that the crlmm outperforms other competing algorithms. In the article, > was the crlmm alg compared to DM alg or Birdseed? Does crlmm perform > better even now when compared to the Birdseed? > > In my case, how should I do the CNV analysis with only 8 samples. Are > there any other packages or adjustments you can suggest me to > compensate for the small sample size? > > Please let me know > Thank you > > On Wed, Mar 17, 2010 at 12:17 PM, Benilton Carvalho > <beniltoncarvalho at="" gmail.com=""> wrote: >> Hi Jeremy, >> >> currently there isn't anything like arrayQualityMetrics implemented in >> oligo/crlmm. >> >> About the sample size, you need at least 10 samples to use >> crlmm::computeCopynumber. >> >> b >> >> On Wed, Mar 17, 2010 at 4:45 PM, jeremy wilson >> <jeremy.wilson88 at="" gmail.com=""> wrote: >>> Dear all, >>> >>> I am wondering if there is a QC methodology like the "contrast QC" >>> check by the affymetrix genome console to QC the arrays before >>> genotyping. The crlmm and Oligo packages do the normalization and >>> summarization which is awesome but I do not see it doing QC checks. I >>> am trying to see the quality of the chips with nice plots similar to >>> that of from "arrayQualityMetrics" package for gene expression arrays. >>> >>> One more question: I have only 8 arrays from the same lab and I need >>> to do LOH and copy number analysis. Will the small number of arrays be >>> problematic? >>> >>> Awaiting for your reply, >>> Thank you >>> JW >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >

ADD REPLY • link 14.7 years ago Benilton Carvalho ★ 4.3k

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Dear Benilton and Henrik, thanks for your suggestions. I read those papers you suggested and am planning to use CRLMM for the genotyping and the aroma.affy package for copy number analysis. Henrik, my data is not a paired sample data. I would need to get a robust average of the 8 samples for the normalization for CNV. I wanted to ask why is there no QC done similar to that of expression arrays? I read that the bg correction is not required for SNP chips as the S/N ratio of intensities is high but I do not see any way to check if the chips are damaged (finger prints, water droplets and etc) due to mishandling by the technicians. Is this check done looking at the genotype calls and their confidence in the downstream analysis? How can I visually see the artifacts? Can I see the effects of normalization with HapMap reference? (Before normalization and after normalization plots). Excuse me for all the questions. I am new to SNP and CNV analysis and am trying to see parallel steps I do in gene expression arrays in SNP chips if that parallelism makes sense at all. Pardon me if it does not.. Any plans to do integrate the genotyping and copy number analysis as done in the BIrdSuite? The paper (http://www.nature.com/ng/journal/v40/n10/abs/ng.237.html) talks about the necessity of this integration. It would be great to see a BioC package doing this as well if you think its needed.. Thanks a lot for your help.. On Thu, Mar 18, 2010 at 3:38 AM, Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> wrote: > Hi Jeremy, > > you may want to take a look at: > > http://www.ncbi.nlm.nih.gov/pubmed/19906825 > http://www.ncbi.nlm.nih.gov/pubmed/18387188 > > in summary, crlmm has been compared to BRLMM, BRLMM-P and, more > recently, to Birdseed. > > Regarding CNV, we currently don't have anything implemented for small > samples in oligo/crlmm. But Henrik already gave you some > suggestions... ;) > > b > > On Wed, Mar 17, 2010 at 8:45 PM, jeremy wilson > <jeremy.wilson88 at="" gmail.com=""> wrote: >> Thanks for the reply dear Benilton.. >> >> how can then one proceed with QC'ing SNP arrays using BioC? >> >> Considering the quality of arrays are good, does the crlmm algorithm >> give good call rates with higher accuracy compared to the Birdseed >> algorithm from Affy genome console and the BirdSuit from Broad MIT? I >> read in one of your papers >> (http://biostatistics.oxfordjournals.org/cgi/content/full/8/2/485) >> that the crlmm outperforms other competing algorithms. In the article, >> was the crlmm alg compared to DM alg or Birdseed? Does crlmm perform >> better even now when compared to the Birdseed? >> >> In my case, how should I do the CNV analysis with only 8 samples. Are >> there any other packages or adjustments you can suggest me to >> compensate for the small sample size? >> >> Please let me know >> Thank you >> >> On Wed, Mar 17, 2010 at 12:17 PM, Benilton Carvalho >> <beniltoncarvalho at="" gmail.com=""> wrote: >>> Hi Jeremy, >>> >>> currently there isn't anything like arrayQualityMetrics implemented in >>> oligo/crlmm. >>> >>> About the sample size, you need at least 10 samples to use >>> crlmm::computeCopynumber. >>> >>> b >>> >>> On Wed, Mar 17, 2010 at 4:45 PM, jeremy wilson >>> <jeremy.wilson88 at="" gmail.com=""> wrote: >>>> Dear all, >>>> >>>> I am wondering if there is a QC methodology like the "contrast QC" >>>> check by the affymetrix genome console to QC the arrays before >>>> genotyping. The crlmm and Oligo packages do the normalization and >>>> summarization which is awesome but I do not see it doing QC checks. I >>>> am trying to see the quality of the chips with nice plots similar to >>>> that of from "arrayQualityMetrics" package for gene expression arrays. >>>> >>>> One more question: I have only 8 arrays from the same lab and I need >>>> to do LOH and copy number analysis. Will the small number of arrays be >>>> problematic? >>>> >>>> Awaiting for your reply, >>>> Thank you >>>> JW >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>> >> >

ADD REPLY • link 14.7 years ago jeremy wilson ▴ 150

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On Tue, Mar 23, 2010 at 8:00 PM, jeremy wilson <jeremy.wilson88 at="" gmail.com=""> wrote: > I wanted to ask why is there no QC done similar to that of expression > arrays? I read that the bg correction is not required for SNP chips as > the S/N ratio of intensities is high but I do not see any way to check > if the chips are damaged (finger prints, water droplets and etc) due > to mishandling by the technicians. Is this check done looking at the > genotype calls and their confidence in the downstream analysis? How > can I visually see the artifacts? Hi Jeremy, I believe one may need to extract the intensitty matrix for the SNP data and work with someyhing like arrayQualityMetrics to get QC going. We have been able to successfully identify problematic arrays by investigating SNR. > Can I see the effects of normalization with HapMap reference? (Before > normalization and after normalization plots). What exactly do you mean? Something like a density plot showing that after normalization the densities across samples are the same? This is possible with the crlmm package, but not straightforward b/c our plan with the pkg is to provide genotype/cn tools. > Any plans to do integrate the genotyping and copy number analysis as > done in the BIrdSuite? The paper > (http://www.nature.com/ng/journal/v40/n10/abs/ng.237.html) talks about > the necessity of this integration. It would be great to see a BioC > package doing this as well if you think its needed.. We are working on something like that (among other things). b > > On Thu, Mar 18, 2010 at 3:38 AM, Benilton Carvalho > <beniltoncarvalho at="" gmail.com=""> wrote: >> Hi Jeremy, >> >> you may want to take a look at: >> >> http://www.ncbi.nlm.nih.gov/pubmed/19906825 >> http://www.ncbi.nlm.nih.gov/pubmed/18387188 >> >> in summary, crlmm has been compared to BRLMM, BRLMM-P and, more >> recently, to Birdseed. >> >> Regarding CNV, we currently don't have anything implemented for small >> samples in oligo/crlmm. But Henrik already gave you some >> suggestions... ;) >> >> b >> >> On Wed, Mar 17, 2010 at 8:45 PM, jeremy wilson >> <jeremy.wilson88 at="" gmail.com=""> wrote: >>> Thanks for the reply dear Benilton.. >>> >>> how can then one proceed with QC'ing SNP arrays using BioC? >>> >>> Considering the quality of arrays are good, does the crlmm algorithm >>> give good call rates with higher accuracy compared to the Birdseed >>> algorithm from Affy genome console and the BirdSuit from Broad MIT? I >>> read in one of your papers >>> (http://biostatistics.oxfordjournals.org/cgi/content/full/8/2/485) >>> that the crlmm outperforms other competing algorithms. In the article, >>> was the crlmm alg compared to DM alg or Birdseed? Does crlmm perform >>> better even now when compared to the Birdseed? >>> >>> In my case, how should I do the CNV analysis with only 8 samples. Are >>> there any other packages or adjustments you can suggest me to >>> compensate for the small sample size? >>> >>> Please let me know >>> Thank you >>> >>> On Wed, Mar 17, 2010 at 12:17 PM, Benilton Carvalho >>> <beniltoncarvalho at="" gmail.com=""> wrote: >>>> Hi Jeremy, >>>> >>>> currently there isn't anything like arrayQualityMetrics implemented in >>>> oligo/crlmm. >>>> >>>> About the sample size, you need at least 10 samples to use >>>> crlmm::computeCopynumber. >>>> >>>> b >>>> >>>> On Wed, Mar 17, 2010 at 4:45 PM, jeremy wilson >>>> <jeremy.wilson88 at="" gmail.com=""> wrote: >>>>> Dear all, >>>>> >>>>> I am wondering if there is a QC methodology like the "contrast QC" >>>>> check by the affymetrix genome console to QC the arrays before >>>>> genotyping. The crlmm and Oligo packages do the normalization and >>>>> summarization which is awesome but I do not see it doing QC checks. I >>>>> am trying to see the quality of the chips with nice plots similar to >>>>> that of from "arrayQualityMetrics" package for gene expression arrays. >>>>> >>>>> One more question: I have only 8 arrays from the same lab and I need >>>>> to do LOH and copy number analysis. Will the small number of arrays be >>>>> problematic? >>>>> >>>>> Awaiting for your reply, >>>>> Thank you >>>>> JW >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at stat.math.ethz.ch >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>> >>>> >>> >> >

ADD REPLY • link 14.7 years ago Benilton Carvalho ★ 4.3k

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Hello all, I have just switched from a Windows PC to a Mac and am having problems installing Bioconductor. I believe the problem is the University proxy server. On Windows, I use the internet2.dll (see 2.19.a in the R for Windows FAQ). This essentially make R connect to the internet through Internet Explorer. Thus, as IE has been configured to work with the University proxy, via an automatic proxy configuration file, R works fine this way too. However, there doesn't seem to be an equivalent option for Mac. Furthermore, I don't know the proxy server details as browsers are configured using an automatic proxy configuration file, rather than by manually setting a proxy server. My questions are: 1) Is there an internet2.dll equivalent for Mac, so I can point R/Bioconductor through Safari? 2) If not, can R/Bioconductor use an automatic proxy configuration file to determine the correct proxy server details? Thanks for your help. Regards, Jonathan ASSOCIATE PROFESSOR JONATHAN ARTHUR Discipline of Medicine | Sydney Medical School THE UNIVERSITY OF SYDNEY Room 141, Medical Foundation Building K25 | The University of Sydney | NSW | 2006 T +61 2 9036 3132 | F +61 2 9036 3233 | M +61 425 397 698 E jonathan.arthur at sydney.edu.au | W http://sydney.edu.au CRICOS 00026A This email plus any attachments to it are confidential. Any unauthorised use is strictly prohibited. If you receive this email in error, please delete it and any attachments. Please think of our environment and only print this e-mail if necessary.

ADD REPLY • link 14.7 years ago Jonathan Arthur ▴ 20

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