Affymetrix 500k SNP chips -- copy number/LOH/deletions
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@stephen-henderson-71
Last seen 7.7 years ago
Is there software for analysing copy number/LOH/deletions in SNP data using R/Bioconductor? Plus apologies for being slightly off-topic but Does anyone know what typical Call rates are for a good analysis of 500k SNP chips? I have calls from about 87-95%, and have heard that 93% is good for 100k chips. Is this range acceptable/ usual for 500k chips? Stephen Henderson Wolfson Inst. for Biomedical Research Cruciform Bldg., Gower Street University College London United Kingdom, WC1E 6BT +44 (0)207 679 6827 ********************************************************************** This email and any files transmitted with it are confidentia...{{dropped}}
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@sean-davis-490
Last seen 4 months ago
United States
On 8/17/06 8:36 AM, "Stephen Henderson" <s.henderson at="" ucl.ac.uk=""> wrote: > Is there software for analysing copy number/LOH/deletions in SNP data > using R/Bioconductor? Benilton will probably reply directly, but you might look at the oligo package. > Plus apologies for being slightly off-topic but > > Does anyone know what typical Call rates are for a good analysis of 500k > SNP chips? I have calls from about 87-95%, and have heard that 93% is > good for 100k chips. Is this range acceptable/ usual for 500k chips? What allele-calling software are you using that is giving those rates? Sean
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@benilton-carvalho-1375
Last seen 4.7 years ago
Brazil/Campinas/UNICAMP
Hi Stephen, the oligo package http://www.bioconductor.org/packages/1.9/bioc/ provides tools for dealing with the SNP arrays. We do not have anything ready for CNA as for now, but you can start exploring your data. You will need also the Platform Design Environments available at: http://www.biostat.jhsph.edu/~bcarvalh/research.html Please, let me know if you need anything else. b On Aug 17, 2006, at 8:36 AM, Stephen Henderson wrote: > Is there software for analysing copy number/LOH/deletions in SNP data > using R/Bioconductor? > > Plus apologies for being slightly off-topic but > > Does anyone know what typical Call rates are for a good analysis of > 500k > SNP chips? I have calls from about 87-95%, and have heard that 93% is > good for 100k chips. Is this range acceptable/ usual for 500k chips? > > > Stephen Henderson > Wolfson Inst. for Biomedical Research > Cruciform Bldg., Gower Street > University College London > United Kingdom, WC1E 6BT > +44 (0)207 679 6827
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@james-w-macdonald-5106
Last seen 2 days ago
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Hi Stephen, Stephen Henderson wrote: > Is there software for analysing copy number/LOH/deletions in SNP data > using R/Bioconductor? > > Plus apologies for being slightly off-topic but > > Does anyone know what typical Call rates are for a good analysis of 500k > SNP chips? I have calls from about 87-95%, and have heard that 93% is > good for 100k chips. Is this range acceptable/ usual for 500k chips? For the 100K chips, and assuming you are using the Affy software (GCOS/GDAS/GTYPE), you should be getting > 95% call rates. This is not possible for the 500K chips, so you have to adjust a setting - I believe it is the homozygote/heterozygote call thresholds - from 0.25 to 0.33 in order to get a call rate in the 90th percentile. This is why Affy has switched from using their maximum likelihood estimation method (they call DM) to BRLMM, which has a higher call rate for the larger chips. CRLMM, which is implemented in the oligo package, probably has higher call rates than either of these two. Note that the current implementation of oligo/makePlatformDesign requires _lots_ of RAM for even a small number of chips, so you will need at the very least a 64 bit OS and more RAM than I have (8 Gb). Best, Jim > > > Stephen Henderson > Wolfson Inst. for Biomedical Research > Cruciform Bldg., Gower Street > University College London > United Kingdom, WC1E 6BT > +44 (0)207 679 6827 > > > > > ********************************************************************** > This email and any files transmitted with it are confidentia...{{dropped}} > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
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@stephen-henderson-71
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dChipSNP might be more memory friendly. Stephen Henderson wrote: > That call rate is from Affymetrix own GTYPE software. > > I did not run the analysis but I believe that the NoCall threshold is below 0.33 confidence. > > I have tried Beniltons software but sadly found I did not not have enough memory. > > -----Original Message----- > From: Sean Davis [mailto:sdavis2 at mail.nih.gov] > Sent: Thu 8/17/2006 1:41 PM > To: Stephen Henderson; Bioconductor > Subject: Re: [BioC] Affymetrix 500k SNP chips -- copy number/LOH/deletions > > > > > On 8/17/06 8:36 AM, "Stephen Henderson" <s.henderson at="" ucl.ac.uk=""> wrote: > > >>Is there software for analysing copy number/LOH/deletions in SNP data >>using R/Bioconductor? > > > Benilton will probably reply directly, but you might look at the oligo > package. > > >>Plus apologies for being slightly off-topic but >> >>Does anyone know what typical Call rates are for a good analysis of 500k >>SNP chips? I have calls from about 87-95%, and have heard that 93% is >>good for 100k chips. Is this range acceptable/ usual for 500k chips? > > > What allele-calling software are you using that is giving those rates? > > Sean > > > > ********************************************************************** > This email and any files transmitted with it are confidentia...{{dropped}} > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
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What's the configuration you have available? We're working on solutions to make it more memory efficient. b On Aug 17, 2006, at 9:25 AM, Stephen Henderson wrote: > That call rate is from Affymetrix own GTYPE software. > > I did not run the analysis but I believe that the NoCall threshold > is below 0.33 confidence. > > I have tried Beniltons software but sadly found I did not not have > enough memory. > > -----Original Message----- > From: Sean Davis [mailto:sdavis2 at mail.nih.gov] > Sent: Thu 8/17/2006 1:41 PM > To: Stephen Henderson; Bioconductor > Subject: Re: [BioC] Affymetrix 500k SNP chips -- copy number/LOH/ > deletions > > > > > On 8/17/06 8:36 AM, "Stephen Henderson" <s.henderson at="" ucl.ac.uk=""> wrote: > >> Is there software for analysing copy number/LOH/deletions in SNP data >> using R/Bioconductor? > > Benilton will probably reply directly, but you might look at the oligo > package. > >> Plus apologies for being slightly off-topic but >> >> Does anyone know what typical Call rates are for a good analysis >> of 500k >> SNP chips? I have calls from about 87-95%, and have heard that 93% is >> good for 100k chips. Is this range acceptable/ usual for 500k chips? > > What allele-calling software are you using that is giving those rates? > > Sean > > > > ********************************************************************** > This email and any files transmitted with it are confidentia... > {{dropped}} > > _______________________________________________ > 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
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@stephen-henderson-71
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On 8/17/06 9:34 AM, "Stephen Henderson" <s.henderson at="" ucl.ac.uk=""> wrote: > I have 4Gb of memory and I'm running linux. Unfortunately its not 64-bit so Im > not sure if R can even use all that memory. I understand that 8Gb is the > maximum even on 64-bit though, is that not true? I don't think that is true in general, but it could be true for your hardware, I suppose. Sean
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Sean Davis wrote: > > > On 8/17/06 9:34 AM, "Stephen Henderson" <s.henderson at="" ucl.ac.uk=""> wrote: > > >>I have 4Gb of memory and I'm running linux. Unfortunately its not 64-bit so Im >>not sure if R can even use all that memory. I understand that 8Gb is the >>maximum even on 64-bit though, is that not true? > > > I don't think that is true in general, but it could be true for your > hardware, I suppose. No it's not true. A 32 bit OS can address 2^32 bits of RAM, whereas a 64 bit OS can address 2^64 bits of RAM (1.84 x 10^13 Gb). As Sean notes, this is hardware dependent - for instance, the box on my desk right now can only take 16 Gb RAM in 8 X 2Gb sticks. However there are comps that will hold enough RAM that percentage-wise, the only real cost is for the RAM itself. Jim > > Sean > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
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errr, on second thought, I think it is more like 1.72 x 10^10 Gb RAM, but what's 3 orders of magnitude between friends? ;-D James W. MacDonald wrote: > Sean Davis wrote: > >> >>On 8/17/06 9:34 AM, "Stephen Henderson" <s.henderson at="" ucl.ac.uk=""> wrote: >> >> >> >>>I have 4Gb of memory and I'm running linux. Unfortunately its not 64-bit so Im >>>not sure if R can even use all that memory. I understand that 8Gb is the >>>maximum even on 64-bit though, is that not true? >> >> >>I don't think that is true in general, but it could be true for your >>hardware, I suppose. > > > No it's not true. A 32 bit OS can address 2^32 bits of RAM, whereas a 64 > bit OS can address 2^64 bits of RAM (1.84 x 10^13 Gb). As Sean notes, > this is hardware dependent - for instance, the box on my desk right now > can only take 16 Gb RAM in 8 X 2Gb sticks. However there are comps that > will hold enough RAM that percentage-wise, the only real cost is for the > RAM itself. > > Jim > > > >>Sean >> >>_______________________________________________ >>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 > > > -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
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