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}}

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

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

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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