SNP Analysis
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Peter Ganske ▴ 50
@peter-ganske-3745
Last seen 10.2 years ago
Hello, first time for me to work with SNP arrays. I got CEL- and CHP-files for my Analysis. The CEL are from Affymetrix Human-Wide Genome SNP- Array 6.0 and the CHP- files are dealed with the Birdseed- Algorithm (part of the Genotyp Console from Affymetrix as well). Is there anybody here, who worked with this arrays in the past? I am looking for an (general) workflow for my study. I want to analyse patients with Rheumatoid Arthritis with regard to SNPs and the question "why there are respoonder and non-responder for the therapy"? I am looking for an workflow for the arrays. Is it better to work with the CHP files or with the CEL- files? Would me great, if anybody can help me out. Thanks in advance Peter The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system. [[alternative HTML version deleted]]
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@vincent-j-carey-jr-4
Last seen 10 weeks ago
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Briefly, you can perform genotype calling with a confidence measure using crlmm package, working from the CEL files. The crlmm package includes a vignette called crlmmDownstream.pdf that illustrates one approach to GWAS analysis based on 6.0, using snpMatrix package. To use crlmm you will also need a metadata package called genomewidesnp6crlmm. There are certainly other approaches possible. Our workflow documentation for this use case probably needs some enhancement. On Wed, Oct 21, 2009 at 9:42 AM, Peter Ganske <peter.ganske at="" hki-="" jena.de=""> wrote: > > Hello, > first time for me to work with SNP arrays. I got CEL- and CHP-files for my Analysis. The CEL are from Affymetrix Human-Wide Genome SNP- Array 6.0 and the CHP- files are dealed with the Birdseed- Algorithm (part of the Genotyp Console from Affymetrix as well). > Is there anybody here, who worked with this arrays in the past? I am looking for an (general) workflow for my study. I want to analyse patients with Rheumatoid Arthritis with regard to SNPs and the question "why there are respoonder and non-responder for the therapy"? > I am looking for an workflow for the arrays. Is it better to work with the CHP files or with the CEL- files? > Would me great, if anybody can help me out. > Thanks in advance > Peter > > > The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system. > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > 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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Dear Vincent, thanks for the fast replay. Well, i thought, that the Genotyping console used the Birdseed Algorithm and this algorithm is an Genotyping Algorithm. Its hard to find paper or groups, who worked with this array and for me ( i work as a student for an institue) is hard to find the right workflow without help (nobody worked here with SNP arrays in the past) So, i have 100 Arrays (100 CHP and 100 CEL files) of 100 patients. I want to have a look at the SNPs of the patients. 50 are non-responder and 50 are responder. There should be a difference between the two groups. Since yet, i looked for any papers for getting an "general" workflow for sorting out most of the SNPs of the patients. So you think i have to try this package and create the genotyping calls? Whats about this workflow? So are my following thought right: - The package check every SNP for every Chips and put the result in a table - i can combine the result of the SNPs with a selection of gene i want.... My boss talked about a top-list of 50 genes... Maybe this can help me out for the usage of CRLMM.. dont know Thanks a lot and sorry for the questions. First time for me to work with SNP Arrays and the first time to work with Bioconductor/R All the best from Germany Peter Am 21.10.2009 um 16:11 schrieb Vincent Carey: > > > Briefly, you can perform genotype calling with a confidence measure > using crlmm package, working from the CEL files. The crlmm package > includes a vignette called crlmmDownstream.pdf that illustrates one > approach to GWAS analysis based on 6.0, using snpMatrix package. To > use crlmm you will also need a metadata package called > genomewidesnp6crlmm. > > There are certainly other approaches possible. Our workflow > documentation for this use case probably needs some enhancement. > > On Wed, Oct 21, 2009 at 9:42 AM, Peter Ganske <peter.ganske@hki- jena.de=""> > wrote: >> >> Hello, >> first time for me to work with SNP arrays. I got CEL- and CHP-files >> for my Analysis. The CEL are from Affymetrix Human-Wide Genome SNP- >> Array 6.0 and the CHP- files are dealed with the Birdseed- >> Algorithm (part of the Genotyp Console from Affymetrix as well). >> Is there anybody here, who worked with this arrays in the past? I >> am looking for an (general) workflow for my study. I want to >> analyse patients with Rheumatoid Arthritis with regard to SNPs and >> the question "why there are respoonder and non-responder for the >> therapy"? >> I am looking for an workflow for the arrays. Is it better to work >> with the CHP files or with the CEL- files? >> Would me great, if anybody can help me out. >> Thanks in advance >> Peter >> >> >> The information contained in this email and any attachments is >> confidential and may be subject to copyright or other intellectual >> property protection. If you are not the intended recipient, you are >> not authorized to use or disclose this information, and we request >> that you notify us by reply mail or telephone and delete the >> original message from your mail system. >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > The information contained in this email and any attachments is > confidential and may be subject to copyright or other intellectual > property protection. If you are not the intended recipient, you are > not authorized to use or disclose this information, and we request > that you notify us by reply mail or telephone and delete the > original message from your mail system. > > The information contained in this email and any attachments is > confidential and may be subject to copyright or other intellectual > property protection. If you are not the intended recipient, you are > not authorized to use or disclose this information, and we request > that you notify us by reply mail or telephone and delete the > original message from your mail system. [[alternative HTML version deleted]]
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Dear Peter, indeed, Birdseed is a genotyping algorithm and I'd use it for genotype calling of SNP6.0 arrays (best suited for this platform). If you have the calls, export them into a table (export options and formats should be described in the Genotyping Console manual) and analyze the genotype frequency differences between responders and non-responders (valuable free software is e.g. PLINK). However, n=100 is a pretty small sample size for a GWAS... Bests, Claus-J?rgen Peter Ganske schrieb: > Dear Vincent, > thanks for the fast replay. Well, i thought, that the Genotyping > console used the Birdseed Algorithm and this algorithm is an > Genotyping Algorithm. > > Its hard to find paper or groups, who worked with this array and for > me ( i work as a student for an institue) is hard to find the right > workflow without help (nobody worked here with SNP arrays in the past) > > So, i have 100 Arrays (100 CHP and 100 CEL files) of 100 patients. I > want to have a look at the SNPs of the patients. 50 are non- responder > and 50 are responder. There should be a difference between the two > groups. Since yet, i looked for any papers for getting an "general" > workflow for sorting out most of the SNPs of the patients. > > So you think i have to try this package and create the genotyping calls? > Whats about this workflow? So are my following thought right: > > - The package check every SNP for every Chips and put the result in a > table > - i can combine the result of the SNPs with a selection of gene i > want.... > > My boss talked about a top-list of 50 genes... Maybe this can help me > out for the usage of CRLMM.. dont know > > Thanks a lot and sorry for the questions. First time for me to work > with SNP Arrays and the first time to work with Bioconductor/R > All the best from Germany > Peter > Am 21.10.2009 um 16:11 schrieb Vincent Carey: > > >> Briefly, you can perform genotype calling with a confidence measure >> using crlmm package, working from the CEL files. The crlmm package >> includes a vignette called crlmmDownstream.pdf that illustrates one >> approach to GWAS analysis based on 6.0, using snpMatrix package. To >> use crlmm you will also need a metadata package called >> genomewidesnp6crlmm. >> >> There are certainly other approaches possible. Our workflow >> documentation for this use case probably needs some enhancement. >> >> On Wed, Oct 21, 2009 at 9:42 AM, Peter Ganske <peter.ganske at="" hki-="" jena.de="">> >>> wrote: >>> >>> Hello, >>> first time for me to work with SNP arrays. I got CEL- and CHP- files >>> for my Analysis. The CEL are from Affymetrix Human-Wide Genome SNP- >>> Array 6.0 and the CHP- files are dealed with the Birdseed- >>> Algorithm (part of the Genotyp Console from Affymetrix as well). >>> Is there anybody here, who worked with this arrays in the past? I >>> am looking for an (general) workflow for my study. I want to >>> analyse patients with Rheumatoid Arthritis with regard to SNPs and >>> the question "why there are respoonder and non-responder for the >>> therapy"? >>> I am looking for an workflow for the arrays. Is it better to work >>> with the CHP files or with the CEL- files? >>> Would me great, if anybody can help me out. >>> Thanks in advance >>> Peter >>> >>> >>> The information contained in this email and any attachments is >>> confidential and may be subject to copyright or other intellectual >>> property protection. If you are not the intended recipient, you are >>> not authorized to use or disclose this information, and we request >>> that you notify us by reply mail or telephone and delete the >>> original message from your mail system. >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> 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 >>> >>> >> The information contained in this email and any attachments is >> confidential and may be subject to copyright or other intellectual >> property protection. If you are not the intended recipient, you are >> not authorized to use or disclose this information, and we request >> that you notify us by reply mail or telephone and delete the >> original message from your mail system. >> >> The information contained in this email and any attachments is >> confidential and may be subject to copyright or other intellectual >> property protection. If you are not the intended recipient, you are >> not authorized to use or disclose this information, and we request >> that you notify us by reply mail or telephone and delete the >> original message from your mail system. >> > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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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Dear Claus- J?rgen, thanks for the reply. In which way you would analyze the genotype frequency wit PLINK? And why you use this program instead of any bioconductor- package? All the best and thanks in advance Peter Am 22.10.2009 um 13:13 schrieb Claus-J?rgen Scholz: > > Dear Peter, > > indeed, Birdseed is a genotyping algorithm and I'd use it for genotype > calling of SNP6.0 arrays (best suited for this platform). If you have > the calls, export them into a table (export options and formats should > be described in the Genotyping Console manual) and analyze the > genotype > frequency differences between responders and non-responders (valuable > free software is e.g. PLINK). However, n=100 is a pretty small sample > size for a GWAS... > > Bests, > Claus-J?rgen > > > Peter Ganske schrieb: >> Dear Vincent, >> thanks for the fast replay. Well, i thought, that the Genotyping >> console used the Birdseed Algorithm and this algorithm is an >> Genotyping Algorithm. >> >> Its hard to find paper or groups, who worked with this array and for >> me ( i work as a student for an institue) is hard to find the right >> workflow without help (nobody worked here with SNP arrays in the >> past) >> >> So, i have 100 Arrays (100 CHP and 100 CEL files) of 100 patients. I >> want to have a look at the SNPs of the patients. 50 are non- responder >> and 50 are responder. There should be a difference between the two >> groups. Since yet, i looked for any papers for getting an "general" >> workflow for sorting out most of the SNPs of the patients. >> >> So you think i have to try this package and create the genotyping >> calls? >> Whats about this workflow? So are my following thought right: >> >> - The package check every SNP for every Chips and put the result in a >> table >> - i can combine the result of the SNPs with a selection of gene i >> want.... >> >> My boss talked about a top-list of 50 genes... Maybe this can help me >> out for the usage of CRLMM.. dont know >> >> Thanks a lot and sorry for the questions. First time for me to work >> with SNP Arrays and the first time to work with Bioconductor/R >> All the best from Germany >> Peter >> Am 21.10.2009 um 16:11 schrieb Vincent Carey: >> >> >>> Briefly, you can perform genotype calling with a confidence measure >>> using crlmm package, working from the CEL files. The crlmm package >>> includes a vignette called crlmmDownstream.pdf that illustrates one >>> approach to GWAS analysis based on 6.0, using snpMatrix package. To >>> use crlmm you will also need a metadata package called >>> genomewidesnp6crlmm. >>> >>> There are certainly other approaches possible. Our workflow >>> documentation for this use case probably needs some enhancement. >>> >>> On Wed, Oct 21, 2009 at 9:42 AM, Peter Ganske <peter.ganske at="" hki-jena.de="">>> >>>> wrote: >>>> >>>> Hello, >>>> first time for me to work with SNP arrays. I got CEL- and CHP- files >>>> for my Analysis. The CEL are from Affymetrix Human-Wide Genome SNP- >>>> Array 6.0 and the CHP- files are dealed with the Birdseed- >>>> Algorithm (part of the Genotyp Console from Affymetrix as well). >>>> Is there anybody here, who worked with this arrays in the past? I >>>> am looking for an (general) workflow for my study. I want to >>>> analyse patients with Rheumatoid Arthritis with regard to SNPs and >>>> the question "why there are respoonder and non-responder for the >>>> therapy"? >>>> I am looking for an workflow for the arrays. Is it better to work >>>> with the CHP files or with the CEL- files? >>>> Would me great, if anybody can help me out. >>>> Thanks in advance >>>> Peter >>>> >>>> >>>> The information contained in this email and any attachments is >>>> confidential and may be subject to copyright or other intellectual >>>> property protection. If you are not the intended recipient, you are >>>> not authorized to use or disclose this information, and we request >>>> that you notify us by reply mail or telephone and delete the >>>> original message from your mail system. >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> 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 >>>> >>>> >>> The information contained in this email and any attachments is >>> confidential and may be subject to copyright or other intellectual >>> property protection. If you are not the intended recipient, you are >>> not authorized to use or disclose this information, and we request >>> that you notify us by reply mail or telephone and delete the >>> original message from your mail system. >>> >>> The information contained in this email and any attachments is >>> confidential and may be subject to copyright or other intellectual >>> property protection. If you are not the intended recipient, you are >>> not authorized to use or disclose this information, and we request >>> that you notify us by reply mail or telephone and delete the >>> original message from your mail system. >>> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 >> > > _______________________________________________ > 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 > > The information contained in this email and any attachments is > confidential and may be subject to copyright or other intellectual > property protection. If you are not the intended recipient, you are > not authorized to use or disclose this information, and we request > that you notify us by reply mail or telephone and delete the > original message from your mail system.
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For a comparison of crlmm (Bioconductor) and birdseed, see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2643934/ There are various interfaces between plink and R. snpMatrix and SNPchip in Bioconductor should also be considered as one thinks about workflows for snp arrays. On Thu, Oct 22, 2009 at 8:51 AM, Peter Ganske <peterganske at="" mac.com=""> wrote: > Dear Claus- J?rgen, > thanks for the reply. In which way you would analyze the genotype frequency > wit PLINK? > And why you use this program instead of any bioconductor- package? > All the best and thanks in advance > Peter > > > > Am 22.10.2009 um 13:13 schrieb Claus-J?rgen Scholz: > >> >> Dear Peter, >> >> indeed, Birdseed is a genotyping algorithm and I'd use it for genotype >> calling of SNP6.0 arrays (best suited for this platform). If you have >> the calls, export them into a table (export options and formats should >> be described in the Genotyping Console manual) and analyze the genotype >> frequency differences between responders and non-responders (valuable >> free software is e.g. PLINK). However, n=100 is a pretty small sample >> size for a GWAS... >> >> Bests, >> Claus-J?rgen >> >> >> Peter Ganske schrieb: >>> >>> Dear Vincent, >>> thanks for the fast replay. Well, i thought, that the Genotyping >>> console used the Birdseed Algorithm and this algorithm is an >>> Genotyping Algorithm. >>> >>> Its hard to find paper or groups, who worked with this array and for >>> me ( i work as a student for an institue) is hard to find the right >>> workflow without help (nobody worked here with SNP arrays in the past) >>> >>> So, i have 100 Arrays (100 CHP and ?100 CEL files) of 100 patients. I >>> want to have a look at the SNPs of the patients. 50 are non- responder >>> and 50 are responder. There should be a difference between the two >>> groups. Since yet, i looked for any papers for getting an "general" >>> workflow for sorting out most of the SNPs of the patients. >>> >>> So you think i have to try this package and create the genotyping calls? >>> Whats about this workflow? So are my following thought right: >>> >>> - The package check every SNP for every Chips and put the result in a >>> table >>> - i can combine the result of the SNPs with a selection of gene i >>> want.... >>> >>> My boss talked about a top-list of 50 genes... Maybe this can help me >>> out for the usage of CRLMM.. dont know >>> >>> Thanks a lot and sorry for the questions. First time for me to work >>> with SNP Arrays and the first time to work with Bioconductor/R >>> All the best from Germany >>> Peter >>> Am 21.10.2009 um 16:11 schrieb Vincent Carey: >>> >>> >>>> Briefly, you can perform genotype calling with a confidence measure >>>> using crlmm package, working from the CEL files. ? The crlmm package >>>> includes a vignette called crlmmDownstream.pdf that illustrates one >>>> approach to GWAS analysis based on 6.0, using snpMatrix package. ?To >>>> use crlmm you will also need a metadata package called >>>> genomewidesnp6crlmm. >>>> >>>> There are certainly other approaches possible. ?Our workflow >>>> documentation for this use case probably needs some enhancement. >>>> >>>> On Wed, Oct 21, 2009 at 9:42 AM, Peter Ganske <peter.ganske at="" hki-jena.de="">>>> >>>>> wrote: >>>>> >>>>> Hello, >>>>> first time for me to work with SNP arrays. I got CEL- and CHP- files >>>>> for my Analysis. The CEL are from Affymetrix Human-Wide Genome SNP- >>>>> Array 6.0 and the CHP- files are dealed with the Birdseed- >>>>> Algorithm (part of the Genotyp Console from Affymetrix as well). >>>>> Is there anybody here, who worked with this arrays in the past? I >>>>> am looking for an (general) workflow for my study. I want to >>>>> analyse patients with Rheumatoid Arthritis with regard to SNPs and >>>>> the question "why there are respoonder and non-responder for the >>>>> therapy"? >>>>> I am looking for an workflow for the arrays. Is it better to work >>>>> with the CHP files or with the CEL- files? >>>>> Would me great, if anybody can help me out. >>>>> Thanks in advance >>>>> Peter >>>>> >>>>> >>>>> The information contained in this email and any attachments is >>>>> confidential and may be subject to copyright or other intellectual >>>>> property protection. If you are not the intended recipient, you are >>>>> not authorized to use or disclose this information, and we request >>>>> that you notify us by reply mail or telephone and delete the >>>>> original message from your mail system. >>>>> ? ? ?[[alternative HTML version deleted]] >>>>> >>>>> _______________________________________________ >>>>> 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 >>>>> >>>>> >>>> The information contained in this email and any attachments is >>>> confidential and may be subject to copyright or other intellectual >>>> property protection. If you are not the intended recipient, you are >>>> not authorized to use or disclose this information, and we request >>>> that you notify us by reply mail or telephone and delete the >>>> original message from your mail system. >>>> >>>> The information contained in this email and any attachments is >>>> confidential and may be subject to copyright or other intellectual >>>> property protection. If you are not the intended recipient, you are >>>> not authorized to use or disclose this information, and we request >>>> that you notify us by reply mail or telephone and delete the >>>> original message from your mail system. >>>> >>> >>> >>> ? ? ? ?[[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> 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 >>> >> >> _______________________________________________ >> 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 >> >> The information contained in this email and any attachments is >> confidential and may be subject to copyright or other intellectual property >> protection. If you are not the intended recipient, you are not authorized to >> use or disclose this information, and we request that you notify us by reply >> mail or telephone and delete the original message from your mail system. > > _______________________________________________ > 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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The following may also be of interest: http://www.bepress.com/jhubiostat/paper180/ b On Oct 22, 2009, at 12:19 PM, Vincent Carey wrote: > For a comparison of crlmm (Bioconductor) and birdseed, see > http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2643934/ > > There are various interfaces between plink and R. snpMatrix and > SNPchip in Bioconductor should also be considered as one thinks about > workflows for snp arrays. > > On Thu, Oct 22, 2009 at 8:51 AM, Peter Ganske <peterganske at="" mac.com=""> > wrote: >> Dear Claus- J?rgen, >> thanks for the reply. In which way you would analyze the genotype >> frequency >> wit PLINK? >> And why you use this program instead of any bioconductor- package? >> All the best and thanks in advance >> Peter >> >> >> >> Am 22.10.2009 um 13:13 schrieb Claus-J?rgen Scholz: >> >>> >>> Dear Peter, >>> >>> indeed, Birdseed is a genotyping algorithm and I'd use it for >>> genotype >>> calling of SNP6.0 arrays (best suited for this platform). If you >>> have >>> the calls, export them into a table (export options and formats >>> should >>> be described in the Genotyping Console manual) and analyze the >>> genotype >>> frequency differences between responders and non-responders >>> (valuable >>> free software is e.g. PLINK). However, n=100 is a pretty small >>> sample >>> size for a GWAS... >>> >>> Bests, >>> Claus-J?rgen >>> >>> >>> Peter Ganske schrieb: >>>> >>>> Dear Vincent, >>>> thanks for the fast replay. Well, i thought, that the Genotyping >>>> console used the Birdseed Algorithm and this algorithm is an >>>> Genotyping Algorithm. >>>> >>>> Its hard to find paper or groups, who worked with this array and >>>> for >>>> me ( i work as a student for an institue) is hard to find the right >>>> workflow without help (nobody worked here with SNP arrays in the >>>> past) >>>> >>>> So, i have 100 Arrays (100 CHP and 100 CEL files) of 100 >>>> patients. I >>>> want to have a look at the SNPs of the patients. 50 are non- >>>> responder >>>> and 50 are responder. There should be a difference between the two >>>> groups. Since yet, i looked for any papers for getting an "general" >>>> workflow for sorting out most of the SNPs of the patients. >>>> >>>> So you think i have to try this package and create the genotyping >>>> calls? >>>> Whats about this workflow? So are my following thought right: >>>> >>>> - The package check every SNP for every Chips and put the result >>>> in a >>>> table >>>> - i can combine the result of the SNPs with a selection of gene i >>>> want.... >>>> >>>> My boss talked about a top-list of 50 genes... Maybe this can >>>> help me >>>> out for the usage of CRLMM.. dont know >>>> >>>> Thanks a lot and sorry for the questions. First time for me to work >>>> with SNP Arrays and the first time to work with Bioconductor/R >>>> All the best from Germany >>>> Peter >>>> Am 21.10.2009 um 16:11 schrieb Vincent Carey: >>>> >>>> >>>>> Briefly, you can perform genotype calling with a confidence >>>>> measure >>>>> using crlmm package, working from the CEL files. The crlmm >>>>> package >>>>> includes a vignette called crlmmDownstream.pdf that illustrates >>>>> one >>>>> approach to GWAS analysis based on 6.0, using snpMatrix >>>>> package. To >>>>> use crlmm you will also need a metadata package called >>>>> genomewidesnp6crlmm. >>>>> >>>>> There are certainly other approaches possible. Our workflow >>>>> documentation for this use case probably needs some enhancement. >>>>> >>>>> On Wed, Oct 21, 2009 at 9:42 AM, Peter Ganske <peter.ganske at="" hki-jena.de="">>>>> >>>>>> wrote: >>>>>> >>>>>> Hello, >>>>>> first time for me to work with SNP arrays. I got CEL- and CHP- >>>>>> files >>>>>> for my Analysis. The CEL are from Affymetrix Human-Wide Genome >>>>>> SNP- >>>>>> Array 6.0 and the CHP- files are dealed with the Birdseed- >>>>>> Algorithm (part of the Genotyp Console from Affymetrix as well). >>>>>> Is there anybody here, who worked with this arrays in the past? I >>>>>> am looking for an (general) workflow for my study. I want to >>>>>> analyse patients with Rheumatoid Arthritis with regard to SNPs >>>>>> and >>>>>> the question "why there are respoonder and non-responder for the >>>>>> therapy"? >>>>>> I am looking for an workflow for the arrays. Is it better to work >>>>>> with the CHP files or with the CEL- files? >>>>>> Would me great, if anybody can help me out. >>>>>> Thanks in advance >>>>>> Peter >>>>>> >>>>>> >>>>>> The information contained in this email and any attachments is >>>>>> confidential and may be subject to copyright or other >>>>>> intellectual >>>>>> property protection. If you are not the intended recipient, you >>>>>> are >>>>>> not authorized to use or disclose this information, and we >>>>>> request >>>>>> that you notify us by reply mail or telephone and delete the >>>>>> original message from your mail system. >>>>>> [[alternative HTML version deleted]] >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>>>> >>>>>> >>>>> The information contained in this email and any attachments is >>>>> confidential and may be subject to copyright or other intellectual >>>>> property protection. If you are not the intended recipient, you >>>>> are >>>>> not authorized to use or disclose this information, and we request >>>>> that you notify us by reply mail or telephone and delete the >>>>> original message from your mail system. >>>>> >>>>> The information contained in this email and any attachments is >>>>> confidential and may be subject to copyright or other intellectual >>>>> property protection. If you are not the intended recipient, you >>>>> are >>>>> not authorized to use or disclose this information, and we request >>>>> that you notify us by reply mail or telephone and delete the >>>>> original message from your mail system. >>>>> >>>> >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> 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 >>>> >>> >>> _______________________________________________ >>> 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 >>> >>> The information contained in this email and any attachments is >>> confidential and may be subject to copyright or other intellectual >>> property >>> protection. If you are not the intended recipient, you are not >>> authorized to >>> use or disclose this information, and we request that you notify >>> us by reply >>> mail or telephone and delete the original message from your mail >>> system. >> >> _______________________________________________ >> 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 >> > > _______________________________________________ > 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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I have to say R/Bioconductor is my favourite too , but PLINK is just great for GWAS for many reasons. You see PLINK , MACH (other imputation algorithms), HALOVIEW and EIGENSTRAT can all be mixed and matched to some extent and provide a workhorse for QC, association and first stop visualisation. I typically use the output of these into R/Bioconductor. That said there are some neat Bioconductor tools that you can use along side... I probably underutilise those myself , but I recommend highly those "common" tools. Plink binary format for genotype data is very handy. MACH-MACH2DAT can take covariates (at the end of the ped files). If is not clear what you are doing but if you have 100 cases, what are your controls ? are you going to use a historical set ...WTCCC ? As for Birdseed and crlmm.To be honest I do not know if crlmm calls genotype AND copy number variations (like birdsuite, Birdseed is apart of that), would be neat if it did. If you have expression data then genotypes + copy number data might be quite useful to you .... depending on what you are studying. 100 cases is very small but I have seen success with as few as 200 for some specific genetic diseases I would consider 1) Affymetrics own SNP calling to get genotypes + PennCNV( or other) to get copy number variations, easy and most straight forward OR Buidsuite if you feel confident (never tried it, I use Illumina) cause then you get copy number variations straight away. 2) your cases + historical controls do a mini GWAS combine genotypes and QC with plink / eigenstrat for SAMPLES and SNPS ie: SAMPLES check:(stratification, related individuals,missingness,heterozygosity... look for outliers ) SNPS:(MAF , genotyping rate, HWE all need to be filtered on) 3) do straight up affy micro array analysis and check against your mini GWAS 4) Really combine expression and genotypes; Try GGtools (Bioconductor) on you genotypes + expression data OR use plink or MACH2DAT with the expression data as covariates, maybe. Plink has an excellent manual check that out. Note GGtools will not require that you do the mini GWAS as you will only need the cases genotypes I think see that package for details, but still do filtering before you begin. my 2c worth of ideas.... Cheers Paul -----Original Message----- From: Peter Ganske <peterganske@mac.com> To: Claus-J?rgen Scholz <scholz at="" klin-biochem.uni-wuerzburg.de=""> Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] SNP Analysis Date: Thu, 22 Oct 2009 14:51:52 +0200 Dear Claus- J?rgen, thanks for the reply. In which way you would analyze the genotype frequency wit PLINK? And why you use this program instead of any bioconductor- package? All the best and thanks in advance Peter Am 22.10.2009 um 13:13 schrieb Claus-J?rgen Scholz: > > Dear Peter, > > indeed, Birdseed is a genotyping algorithm and I'd use it for genotype > calling of SNP6.0 arrays (best suited for this platform). If you have > the calls, export them into a table (export options and formats should > be described in the Genotyping Console manual) and analyze the > genotype > frequency differences between responders and non-responders (valuable > free software is e.g. PLINK). However, n=100 is a pretty small sample > size for a GWAS... > > Bests, > Claus-J?rgen > > > Peter Ganske schrieb: >> Dear Vincent, >> thanks for the fast replay. Well, i thought, that the Genotyping >> console used the Birdseed Algorithm and this algorithm is an >> Genotyping Algorithm. >> >> Its hard to find paper or groups, who worked with this array and for >> me ( i work as a student for an institue) is hard to find the right >> workflow without help (nobody worked here with SNP arrays in the >> past) >> >> So, i have 100 Arrays (100 CHP and 100 CEL files) of 100 patients. I >> want to have a look at the SNPs of the patients. 50 are non- responder >> and 50 are responder. There should be a difference between the two >> groups. Since yet, i looked for any papers for getting an "general" >> workflow for sorting out most of the SNPs of the patients. >> >> So you think i have to try this package and create the genotyping >> calls? >> Whats about this workflow? So are my following thought right: >> >> - The package check every SNP for every Chips and put the result in a >> table >> - i can combine the result of the SNPs with a selection of gene i >> want.... >> >> My boss talked about a top-list of 50 genes... Maybe this can help me >> out for the usage of CRLMM.. dont know >> >> Thanks a lot and sorry for the questions. First time for me to work >> with SNP Arrays and the first time to work with Bioconductor/R >> All the best from Germany >> Peter >> Am 21.10.2009 um 16:11 schrieb Vincent Carey: >> >> >>> Briefly, you can perform genotype calling with a confidence measure >>> using crlmm package, working from the CEL files. The crlmm package >>> includes a vignette called crlmmDownstream.pdf that illustrates one >>> approach to GWAS analysis based on 6.0, using snpMatrix package. To >>> use crlmm you will also need a metadata package called >>> genomewidesnp6crlmm. >>> >>> There are certainly other approaches possible. Our workflow >>> documentation for this use case probably needs some enhancement. >>> >>> On Wed, Oct 21, 2009 at 9:42 AM, Peter Ganske <peter.ganske at="" hki-jena.de="">>> >>>> wrote: >>>> >>>> Hello, >>>> first time for me to work with SNP arrays. I got CEL- and CHP- files >>>> for my Analysis. The CEL are from Affymetrix Human-Wide Genome SNP- >>>> Array 6.0 and the CHP- files are dealed with the Birdseed- >>>> Algorithm (part of the Genotyp Console from Affymetrix as well). >>>> Is there anybody here, who worked with this arrays in the past? I >>>> am looking for an (general) workflow for my study. I want to >>>> analyse patients with Rheumatoid Arthritis with regard to SNPs and >>>> the question "why there are respoonder and non-responder for the >>>> therapy"? >>>> I am looking for an workflow for the arrays. Is it better to work >>>> with the CHP files or with the CEL- files? >>>> Would me great, if anybody can help me out. >>>> Thanks in advance >>>> Peter >>>> >>>> >>>> The information contained in this email and any attachments is >>>> confidential and may be subject to copyright or other intellectual >>>> property protection. If you are not the intended recipient, you are >>>> not authorized to use or disclose this information, and we request >>>> that you notify us by reply mail or telephone and delete the >>>> original message from your mail system. >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> 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 >>>> >>>> >>> The information contained in this email and any attachments is >>> confidential and may be subject to copyright or other intellectual >>> property protection. If you are not the intended recipient, you are >>> not authorized to use or disclose this information, and we request >>> that you notify us by reply mail or telephone and delete the >>> original message from your mail system. >>> >>> The information contained in this email and any attachments is >>> confidential and may be subject to copyright or other intellectual >>> property protection. If you are not the intended recipient, you are >>> not authorized to use or disclose this information, and we request >>> that you notify us by reply mail or telephone and delete the >>> original message from your mail system. >>> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 >> > > _______________________________________________ > 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 > > The information contained in this email and any attachments is > confidential and may be subject to copyright or other intellectual > property protection. If you are not the intended recipient, you are > not authorized to use or disclose this information, and we request > that you notify us by reply mail or telephone and delete the > original message from your mail system. _______________________________________________ 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 -- Dr Paul Leo Bioinformatician Diamantina Institute for Cancer, Immunology and Metabolic Medicine University of Queensland ---------------------------------------------------------------------- ---------------- Research Wing, Bldg 1 Princess Alexandria Hospital Woolloongabba, QLD, 4102 Tel: +61 7 3240 7740 Mob: 041 303 8691 Fax: +61 7 3240 5946 Email: p.leo at uq.edu.au Web: http://www.di.uq.edu.au
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Regarding CNA, the 'crlmm' package does include a copy number tool: http://www.bepress.com/jhubiostat/paper197/ http://www.bioconductor.org/packages/2.5/bioc/vignettes/crlmm/inst/doc /copynumber.pdf b On Oct 23, 2009, at 5:03 AM, Paul Leo wrote: > I have to say R/Bioconductor is my favourite too , but PLINK is just > great for GWAS for many reasons. You see PLINK , MACH (other > imputation > algorithms), HALOVIEW and EIGENSTRAT can all be mixed and matched to > some extent and provide a workhorse for QC, association and first stop > visualisation. I typically use the output of these into R/ > Bioconductor. > That said there are some neat Bioconductor tools that you can use > along > side... I probably underutilise those myself , but I recommend highly > those "common" tools. > > Plink binary format for genotype data is very handy. MACH-MACH2DAT can > take covariates (at the end of the ped files). If is not clear what > you > are doing but if you have 100 cases, what are your controls ? are you > going to use a historical set ...WTCCC ? > > As for Birdseed and crlmm.To be honest I do not know if crlmm calls > genotype AND copy number variations (like birdsuite, Birdseed is apart > of that), would be neat if it did. If you have expression data then > genotypes + copy number data might be quite useful to you .... > depending > on what you are studying. > > 100 cases is very small but I have seen success with as few as 200 for > some specific genetic diseases > > I would consider > 1) Affymetrics own SNP calling to get genotypes + PennCNV( or > other) to > get copy number variations, easy and most straight forward > OR > Buidsuite if you feel confident (never tried it, I use Illumina) cause > then you get copy number variations straight away. > > 2) your cases + historical controls do a mini GWAS > combine genotypes and QC with plink / eigenstrat for SAMPLES and SNPS > ie: > > SAMPLES check:(stratification, related > individuals,missingness,heterozygosity... look for outliers ) > > SNPS:(MAF , genotyping rate, HWE all need to be filtered on) > > 3) do straight up affy micro array analysis and check against your > mini > GWAS > > 4) Really combine expression and genotypes; Try GGtools (Bioconductor) > on you genotypes + expression data > OR use plink or MACH2DAT with the expression data as covariates, > maybe. > Plink has an excellent manual check that out. > > Note GGtools will not require that you do the mini GWAS as you will > only need the cases genotypes I think see that package for details, > but > still do filtering before you begin. > > my 2c worth of ideas.... > > Cheers > Paul > > > > > > > > > > > > > -----Original Message----- > From: Peter Ganske <peterganske at="" mac.com=""> > To: Claus-J?rgen Scholz <scholz at="" klin-biochem.uni-wuerzburg.de=""> > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] SNP Analysis > Date: Thu, 22 Oct 2009 14:51:52 +0200 > > Dear Claus- J?rgen, > thanks for the reply. In which way you would analyze the genotype > frequency wit PLINK? > And why you use this program instead of any bioconductor- package? > All the best and thanks in advance > Peter > > > > Am 22.10.2009 um 13:13 schrieb Claus-J?rgen Scholz: > >> >> Dear Peter, >> >> indeed, Birdseed is a genotyping algorithm and I'd use it for >> genotype >> calling of SNP6.0 arrays (best suited for this platform). If you have >> the calls, export them into a table (export options and formats >> should >> be described in the Genotyping Console manual) and analyze the >> genotype >> frequency differences between responders and non-responders (valuable >> free software is e.g. PLINK). However, n=100 is a pretty small sample >> size for a GWAS... >> >> Bests, >> Claus-J?rgen >> >> >> Peter Ganske schrieb: >>> Dear Vincent, >>> thanks for the fast replay. Well, i thought, that the Genotyping >>> console used the Birdseed Algorithm and this algorithm is an >>> Genotyping Algorithm. >>> >>> Its hard to find paper or groups, who worked with this array and for >>> me ( i work as a student for an institue) is hard to find the right >>> workflow without help (nobody worked here with SNP arrays in the >>> past) >>> >>> So, i have 100 Arrays (100 CHP and 100 CEL files) of 100 >>> patients. I >>> want to have a look at the SNPs of the patients. 50 are non- >>> responder >>> and 50 are responder. There should be a difference between the two >>> groups. Since yet, i looked for any papers for getting an "general" >>> workflow for sorting out most of the SNPs of the patients. >>> >>> So you think i have to try this package and create the genotyping >>> calls? >>> Whats about this workflow? So are my following thought right: >>> >>> - The package check every SNP for every Chips and put the result >>> in a >>> table >>> - i can combine the result of the SNPs with a selection of gene i >>> want.... >>> >>> My boss talked about a top-list of 50 genes... Maybe this can help >>> me >>> out for the usage of CRLMM.. dont know >>> >>> Thanks a lot and sorry for the questions. First time for me to work >>> with SNP Arrays and the first time to work with Bioconductor/R >>> All the best from Germany >>> Peter >>> Am 21.10.2009 um 16:11 schrieb Vincent Carey: >>> >>> >>>> Briefly, you can perform genotype calling with a confidence measure >>>> using crlmm package, working from the CEL files. The crlmm >>>> package >>>> includes a vignette called crlmmDownstream.pdf that illustrates one >>>> approach to GWAS analysis based on 6.0, using snpMatrix package. >>>> To >>>> use crlmm you will also need a metadata package called >>>> genomewidesnp6crlmm. >>>> >>>> There are certainly other approaches possible. Our workflow >>>> documentation for this use case probably needs some enhancement. >>>> >>>> On Wed, Oct 21, 2009 at 9:42 AM, Peter Ganske <peter.ganske at="" hki-jena.de="">>>> >>>>> wrote: >>>>> >>>>> Hello, >>>>> first time for me to work with SNP arrays. I got CEL- and CHP- >>>>> files >>>>> for my Analysis. The CEL are from Affymetrix Human-Wide Genome >>>>> SNP- >>>>> Array 6.0 and the CHP- files are dealed with the Birdseed- >>>>> Algorithm (part of the Genotyp Console from Affymetrix as well). >>>>> Is there anybody here, who worked with this arrays in the past? I >>>>> am looking for an (general) workflow for my study. I want to >>>>> analyse patients with Rheumatoid Arthritis with regard to SNPs and >>>>> the question "why there are respoonder and non-responder for the >>>>> therapy"? >>>>> I am looking for an workflow for the arrays. Is it better to work >>>>> with the CHP files or with the CEL- files? >>>>> Would me great, if anybody can help me out. >>>>> Thanks in advance >>>>> Peter >>>>> >>>>> >>>>> The information contained in this email and any attachments is >>>>> confidential and may be subject to copyright or other intellectual >>>>> property protection. If you are not the intended recipient, you >>>>> are >>>>> not authorized to use or disclose this information, and we request >>>>> that you notify us by reply mail or telephone and delete the >>>>> original message from your mail system. >>>>> [[alternative HTML version deleted]] >>>>> >>>>> _______________________________________________ >>>>> 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 >>>>> >>>>> >>>> The information contained in this email and any attachments is >>>> confidential and may be subject to copyright or other intellectual >>>> property protection. If you are not the intended recipient, you are >>>> not authorized to use or disclose this information, and we request >>>> that you notify us by reply mail or telephone and delete the >>>> original message from your mail system. >>>> >>>> The information contained in this email and any attachments is >>>> confidential and may be subject to copyright or other intellectual >>>> property protection. If you are not the intended recipient, you are >>>> not authorized to use or disclose this information, and we request >>>> that you notify us by reply mail or telephone and delete the >>>> original message from your mail system. >>>> >>> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> 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 >>> >> >> _______________________________________________ >> 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 >> >> The information contained in this email and any attachments is >> confidential and may be subject to copyright or other intellectual >> property protection. If you are not the intended recipient, you are >> not authorized to use or disclose this information, and we request >> that you notify us by reply mail or telephone and delete the >> original message from your mail system. > > _______________________________________________ > 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 > -- > Dr Paul Leo > Bioinformatician > Diamantina Institute for Cancer, Immunology and Metabolic Medicine > University of Queensland > -------------------------------------------------------------------- ------------------ > Research Wing, Bldg 1 > Princess Alexandria Hospital > Woolloongabba, QLD, 4102 > Tel: +61 7 3240 7740 Mob: 041 303 8691 Fax: +61 7 3240 5946 > Email: p.leo at uq.edu.au Web: http://www.di.uq.edu.au > > _______________________________________________ > 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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Very nice! Thanks for the heads up. Cheers Paul Date: Fri, 23 Oct 2009 12:10:36 -0200 Regarding CNA, the 'crlmm' package does include a copy number tool: http://www.bepress.com/jhubiostat/paper197/ http://www.bioconductor.org/packages/2.5/bioc/vignettes/crlmm/inst/doc /copynumber.pdf b On Oct 23, 2009, at 5:03 AM, Paul Leo wrote: > I have to say R/Bioconductor is my favourite too , but PLINK is just > great for GWAS for many reasons. You see PLINK , MACH (other > imputation > algorithms), HALOVIEW and EIGENSTRAT can all be mixed and matched to > some extent and provide a workhorse for QC, association and first stop > visualisation. I typically use the output of these into R/ > Bioconductor. > That said there are some neat Bioconductor tools that you can use > along > side... I probably underutilise those myself , but I recommend highly > those "common" tools. > > Plink binary format for genotype data is very handy. MACH-MACH2DAT can > take covariates (at the end of the ped files). If is not clear what > you > are doing but if you have 100 cases, what are your controls ? are you > going to use a historical set ...WTCCC ? > > As for Birdseed and crlmm.To be honest I do not know if crlmm calls > genotype AND copy number variations (like birdsuite, Birdseed is apart > of that), would be neat if it did. If you have expression data then > genotypes + copy number data might be quite useful to you .... > depending > on what you are studying. > > 100 cases is very small but I have seen success with as few as 200 for > some specific genetic diseases > > I would consider > 1) Affymetrics own SNP calling to get genotypes + PennCNV( or > other) to > get copy number variations, easy and most straight forward > OR > Buidsuite if you feel confident (never tried it, I use Illumina) cause > then you get copy number variations straight away. > > 2) your cases + historical controls do a mini GWAS > combine genotypes and QC with plink / eigenstrat for SAMPLES and SNPS > ie: > > SAMPLES check:(stratification, related > individuals,missingness,heterozygosity... look for outliers ) > > SNPS:(MAF , genotyping rate, HWE all need to be filtered on) > > 3) do straight up affy micro array analysis and check against your > mini > GWAS > > 4) Really combine expression and genotypes; Try GGtools (Bioconductor) > on you genotypes + expression data > OR use plink or MACH2DAT with the expression data as covariates, > maybe. > Plink has an excellent manual check that out. > > Note GGtools will not require that you do the mini GWAS as you will > only need the cases genotypes I think see that package for details, > but > still do filtering before you begin. > > my 2c worth of ideas.... > > Cheers > Paul > > > > > > > > > > > > > -----Original Message----- > From: Peter Ganske <peterganske at="" mac.com=""> > To: Claus-J?rgen Scholz <scholz at="" klin-biochem.uni-wuerzburg.de=""> > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] SNP Analysis > Date: Thu, 22 Oct 2009 14:51:52 +0200 > > Dear Claus- J?rgen, > thanks for the reply. In which way you would analyze the genotype > frequency wit PLINK? > And why you use this program instead of any bioconductor- package? > All the best and thanks in advance > Peter > > > > Am 22.10.2009 um 13:13 schrieb Claus-J?rgen Scholz: > >> >> Dear Peter, >> >> indeed, Birdseed is a genotyping algorithm and I'd use it for >> genotype >> calling of SNP6.0 arrays (best suited for this platform). If you have >> the calls, export them into a table (export options and formats >> should >> be described in the Genotyping Console manual) and analyze the >> genotype >> frequency differences between responders and non-responders (valuable >> free software is e.g. PLINK). However, n=100 is a pretty small sample >> size for a GWAS... >> >> Bests, >> Claus-J?rgen >> >> >> Peter Ganske schrieb: >>> Dear Vincent, >>> thanks for the fast replay. Well, i thought, that the Genotyping >>> console used the Birdseed Algorithm and this algorithm is an >>> Genotyping Algorithm. >>> >>> Its hard to find paper or groups, who worked with this array and for >>> me ( i work as a student for an institue) is hard to find the right >>> workflow without help (nobody worked here with SNP arrays in the >>> past) >>> >>> So, i have 100 Arrays (100 CHP and 100 CEL files) of 100 >>> patients. I >>> want to have a look at the SNPs of the patients. 50 are non- >>> responder >>> and 50 are responder. There should be a difference between the two >>> groups. Since yet, i looked for any papers for getting an "general" >>> workflow for sorting out most of the SNPs of the patients. >>> >>> So you think i have to try this package and create the genotyping >>> calls? >>> Whats about this workflow? So are my following thought right: >>> >>> - The package check every SNP for every Chips and put the result >>> in a >>> table >>> - i can combine the result of the SNPs with a selection of gene i >>> want.... >>> >>> My boss talked about a top-list of 50 genes... Maybe this can help >>> me >>> out for the usage of CRLMM.. dont know >>> >>> Thanks a lot and sorry for the questions. First time for me to work >>> with SNP Arrays and the first time to work with Bioconductor/R >>> All the best from Germany >>> Peter >>> Am 21.10.2009 um 16:11 schrieb Vincent Carey: >>> >>> >>>> Briefly, you can perform genotype calling with a confidence measure >>>> using crlmm package, working from the CEL files. The crlmm >>>> package >>>> includes a vignette called crlmmDownstream.pdf that illustrates one >>>> approach to GWAS analysis based on 6.0, using snpMatrix package. >>>> To >>>> use crlmm you will also need a metadata package called >>>> genomewidesnp6crlmm. >>>> >>>> There are certainly other approaches possible. Our workflow >>>> documentation for this use case probably needs some enhancement. >>>> >>>> On Wed, Oct 21, 2009 at 9:42 AM, Peter Ganske <peter.ganske at="" hki-jena.de="">>>> >>>>> wrote: >>>>> >>>>> Hello, >>>>> first time for me to work with SNP arrays. I got CEL- and CHP- >>>>> files >>>>> for my Analysis. The CEL are from Affymetrix Human-Wide Genome >>>>> SNP- >>>>> Array 6.0 and the CHP- files are dealed with the Birdseed- >>>>> Algorithm (part of the Genotyp Console from Affymetrix as well). >>>>> Is there anybody here, who worked with this arrays in the past? I >>>>> am looking for an (general) workflow for my study. I want to >>>>> analyse patients with Rheumatoid Arthritis with regard to SNPs and >>>>> the question "why there are respoonder and non-responder for the >>>>> therapy"? >>>>> I am looking for an workflow for the arrays. Is it better to work >>>>> with the CHP files or with the CEL- files? >>>>> Would me great, if anybody can help me out. >>>>> Thanks in advance >>>>> Peter >>>>> >>>>> >>>>> The information contained in this email and any attachments is >>>>> confidential and may be subject to copyright or other intellectual >>>>> property protection. If you are not the intended recipient, you >>>>> are >>>>> not authorized to use or disclose this information, and we request >>>>> that you notify us by reply mail or telephone and delete the >>>>> original message from your mail system. >>>>> [[alternative HTML version deleted]] >>>>> >>>>> _______________________________________________ >>>>> 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 >>>>> >>>>> >>>> The information contained in this email and any attachments is >>>> confidential and may be subject to copyright or other intellectual >>>> property protection. If you are not the intended recipient, you are >>>> not authorized to use or disclose this information, and we request >>>> that you notify us by reply mail or telephone and delete the >>>> original message from your mail system. >>>> >>>> The information contained in this email and any attachments is >>>> confidential and may be subject to copyright or other intellectual >>>> property protection. If you are not the intended recipient, you are >>>> not authorized to use or disclose this information, and we request >>>> that you notify us by reply mail or telephone and delete the >>>> original message from your mail system. >>>> >>> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> 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 >>> >> >> _______________________________________________ >> 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 >> >> The information contained in this email and any attachments is >> confidential and may be subject to copyright or other intellectual >> property protection. If you are not the intended recipient, you are >> not authorized to use or disclose this information, and we request >> that you notify us by reply mail or telephone and delete the >> original message from your mail system. > > _______________________________________________ > 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 > -- > Dr Paul Leo > Bioinformatician > Diamantina Institute for Cancer, Immunology and Metabolic Medicine > University of Queensland > -------------------------------------------------------------------- ------------------ > Research Wing, Bldg 1 > Princess Alexandria Hospital > Woolloongabba, QLD, 4102 > Tel: +61 7 3240 7740 Mob: 041 303 8691 Fax: +61 7 3240 5946 > Email: p.leo at uq.edu.au Web: http://www.di.uq.edu.au > > _______________________________________________ > 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 -- Dr Paul Leo Bioinformatician Diamantina Institute for Cancer, Immunology and Metabolic Medicine University of Queensland ---------------------------------------------------------------------- ---------------- Research Wing, Bldg 1 Princess Alexandria Hospital Woolloongabba, QLD, 4102 Tel: +61 7 3240 7740 Mob: 041 303 8691 Fax: +61 7 3240 5946 Email: p.leo at uq.edu.au Web: http://www.di.uq.edu.au
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Thanks for all the replies. I will check out some ideas. What systems you used for the CRLMM- Analysis? It would be helpfull, if you can tell me something about the memory i need for this thanks in advance Peter >>> Paul Leo <p.leo@uq.edu.au> 25.10.2009 23:48 >>> Very nice! Thanks for the heads up. Cheers Paul Date: Fri, 23 Oct 2009 12:10:36 -0200 Regarding CNA, the 'crlmm' package does include a copy number tool: http://www.bepress.com/jhubiostat/paper197/ http://www.bioconductor.org/packages/2.5/bioc/vignettes/crlmm/inst/doc /copynumber.pdf b On Oct 23, 2009, at 5:03 AM, Paul Leo wrote: > I have to say R/Bioconductor is my favourite too , but PLINK is just > great for GWAS for many reasons. You see PLINK , MACH (other > imputation > algorithms), HALOVIEW and EIGENSTRAT can all be mixed and matched to > some extent and provide a workhorse for QC, association and first stop > visualisation. I typically use the output of these into R/ > Bioconductor. > That said there are some neat Bioconductor tools that you can use > along > side... I probably underutilise those myself , but I recommend highly > those "common" tools. > > Plink binary format for genotype data is very handy. MACH-MACH2DAT can > take covariates (at the end of the ped files). If is not clear what > you > are doing but if you have 100 cases, what are your controls ? are you > going to use a historical set ...WTCCC ? > > As for Birdseed and crlmm.To be honest I do not know if crlmm calls > genotype AND copy number variations (like birdsuite, Birdseed is apart > of that), would be neat if it did. If you have expression data then > genotypes + copy number data might be quite useful to you .... > depending > on what you are studying. > > 100 cases is very small but I have seen success with as few as 200 for > some specific genetic diseases > > I would consider > 1) Affymetrics own SNP calling to get genotypes + PennCNV( or > other) to > get copy number variations, easy and most straight forward > OR > Buidsuite if you feel confident (never tried it, I use Illumina) cause > then you get copy number variations straight away. > > 2) your cases + historical controls do a mini GWAS > combine genotypes and QC with plink / eigenstrat for SAMPLES and SNPS > ie: > > SAMPLES check:(stratification, related > individuals,missingness,heterozygosity... look for outliers ) > > SNPS:(MAF , genotyping rate, HWE all need to be filtered on) > > 3) do straight up affy micro array analysis and check against your > mini > GWAS > > 4) Really combine expression and genotypes; Try GGtools (Bioconductor) > on you genotypes + expression data > OR use plink or MACH2DAT with the expression data as covariates, > maybe. > Plink has an excellent manual check that out. > > Note GGtools will not require that you do the mini GWAS as you will > only need the cases genotypes I think see that package for details, > but > still do filtering before you begin. > > my 2c worth of ideas.... > > Cheers > Paul > > > > > > > > > > > > > -----Original Message----- > From: Peter Ganske <peterganske@mac.com> > To: Claus-Jürgen Scholz <scholz@klin-biochem.uni-wuerzburg.de> > Cc: bioconductor@stat.math.ethz.ch > Subject: Re: [BioC] SNP Analysis > Date: Thu, 22 Oct 2009 14:51:52 +0200 > > Dear Claus- Jürgen, > thanks for the reply. In which way you would analyze the genotype > frequency wit PLINK? > And why you use this program instead of any bioconductor- package? > All the best and thanks in advance > Peter > > > > Am 22.10.2009 um 13:13 schrieb Claus-Jürgen Scholz: > >> >> Dear Peter, >> >> indeed, Birdseed is a genotyping algorithm and I'd use it for >> genotype >> calling of SNP6.0 arrays (best suited for this platform). If you have >> the calls, export them into a table (export options and formats >> should >> be described in the Genotyping Console manual) and analyze the >> genotype >> frequency differences between responders and non-responders (valuable >> free software is e.g. PLINK). However, n=100 is a pretty small sample >> size for a GWAS... >> >> Bests, >> Claus-Jürgen >> >> >> Peter Ganske schrieb: >>> Dear Vincent, >>> thanks for the fast replay. Well, i thought, that the Genotyping >>> console used the Birdseed Algorithm and this algorithm is an >>> Genotyping Algorithm. >>> >>> Its hard to find paper or groups, who worked with this array and for >>> me ( i work as a student for an institue) is hard to find the right >>> workflow without help (nobody worked here with SNP arrays in the >>> past) >>> >>> So, i have 100 Arrays (100 CHP and 100 CEL files) of 100 >>> patients. I >>> want to have a look at the SNPs of the patients. 50 are non- >>> responder >>> and 50 are responder. There should be a difference between the two >>> groups. Since yet, i looked for any papers for getting an "general" >>> workflow for sorting out most of the SNPs of the patients. >>> >>> So you think i have to try this package and create the genotyping >>> calls? >>> Whats about this workflow? So are my following thought right: >>> >>> - The package check every SNP for every Chips and put the result >>> in a >>> table >>> - i can combine the result of the SNPs with a selection of gene i >>> want.... >>> >>> My boss talked about a top-list of 50 genes... Maybe this can help >>> me >>> out for the usage of CRLMM.. dont know >>> >>> Thanks a lot and sorry for the questions. First time for me to work >>> with SNP Arrays and the first time to work with Bioconductor/R >>> All the best from Germany >>> Peter >>> Am 21.10.2009 um 16:11 schrieb Vincent Carey: >>> >>> >>>> Briefly, you can perform genotype calling with a confidence measure >>>> using crlmm package, working from the CEL files. The crlmm >>>> package >>>> includes a vignette called crlmmDownstream.pdf that illustrates one >>>> approach to GWAS analysis based on 6.0, using snpMatrix package. >>>> To >>>> use crlmm you will also need a metadata package called >>>> genomewidesnp6crlmm. >>>> >>>> There are certainly other approaches possible. Our workflow >>>> documentation for this use case probably needs some enhancement. >>>> >>>> On Wed, Oct 21, 2009 at 9:42 AM, Peter Ganske <peter.ganske@hki-jena.de>>>> >>>>> wrote: >>>>> >>>>> Hello, >>>>> first time for me to work with SNP arrays. I got CEL- and CHP- >>>>> files >>>>> for my Analysis. The CEL are from Affymetrix Human-Wide Genome >>>>> SNP- >>>>> Array 6.0 and the CHP- files are dealed with the Birdseed- >>>>> Algorithm (part of the Genotyp Console from Affymetrix as well). >>>>> Is there anybody here, who worked with this arrays in the past? I >>>>> am looking for an (general) workflow for my study. I want to >>>>> analyse patients with Rheumatoid Arthritis with regard to SNPs and >>>>> the question "why there are respoonder and non-responder for the >>>>> therapy"? >>>>> I am looking for an workflow for the arrays. Is it better to work >>>>> with the CHP files or with the CEL- files? >>>>> Would me great, if anybody can help me out. >>>>> Thanks in advance >>>>> Peter >>>>> >>>>> >>>>> The information contained in this email and any attachments is >>>>> confidential and may be subject to copyright or other intellectual >>>>> property protection. If you are not the intended recipient, you >>>>> are >>>>> not authorized to use or disclose this information, and we request >>>>> that you notify us by reply mail or telephone and delete the >>>>> original message from your mail system. >>>>> [[alternative HTML version deleted]] >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor@stat.math.ethz.ch >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>> >>>>> >>>> The information contained in this email and any attachments is >>>> confidential and may be subject to copyright or other intellectual >>>> property protection. If you are not the intended recipient, you are >>>> not authorized to use or disclose this information, and we request >>>> that you notify us by reply mail or telephone and delete the >>>> original message from your mail system. >>>> >>>> The information contained in this email and any attachments is >>>> confidential and may be subject to copyright or other intellectual >>>> property protection. If you are not the intended recipient, you are >>>> not authorized to use or disclose this information, and we request >>>> that you notify us by reply mail or telephone and delete the >>>> original message from your mail system. >>>> >>> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> The information contained in this email and any attachments is >> confidential and may be subject to copyright or other intellectual >> property protection. If you are not the intended recipient, you are >> not authorized to use or disclose this information, and we request >> that you notify us by reply mail or telephone and delete the >> original message from your mail system. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- > Dr Paul Leo > Bioinformatician > Diamantina Institute for Cancer, Immunology and Metabolic Medicine > University of Queensland > ---------------------------------------------------------------------- ---------------- > Research Wing, Bldg 1 > Princess Alexandria Hospital > Woolloongabba, QLD, 4102 > Tel: +61 7 3240 7740 Mob: 041 303 8691 Fax: +61 7 3240 5946 > Email: p.leo@uq.edu.au Web: http://www.di.uq.edu.au > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Dr Paul Leo Bioinformatician Diamantina Institute for Cancer, Immunology and Metabolic Medicine University of Queensland ---------------------------------------------------------------------- ---------------- Research Wing, Bldg 1 Princess Alexandria Hospital Woolloongabba, QLD, 4102 Tel: +61 7 3240 7740 Mob: 041 303 8691 Fax: +61 7 3240 5946 Email: p.leo@uq.edu.au Web: http://www.di.uq.edu.au _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
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To genotype 100 samples, you'd need somethng like 3GB RAM and the package is available for all platforms. b On Oct 26, 2009, at 8:46 AM, Peter Ganske wrote: > Thanks for all the replies. I will check out some ideas. > What systems you used for the CRLMM- Analysis? It would be helpfull, > if you can tell me something about the memory i need for this > thanks in advance > Peter > > > > >>> Paul Leo <p.leo at="" uq.edu.au=""> 25.10.2009 23:48 >>> > Very nice! > Thanks for the heads up. > Cheers > Paul > > > Date: Fri, 23 Oct 2009 12:10:36 -0200 > > Regarding CNA, the 'crlmm' package does include a copy number tool: > > http://www.bepress.com/jhubiostat/paper197/ > http://www.bioconductor.org/packages/2.5/bioc/vignettes/crlmm/inst/d oc/copynumber.pdf > > b > > On Oct 23, 2009, at 5:03 AM, Paul Leo wrote: > > > I have to say R/Bioconductor is my favourite too , but PLINK is just > > great for GWAS for many reasons. You see PLINK , MACH (other > > imputation > > algorithms), HALOVIEW and EIGENSTRAT can all be mixed and matched to > > some extent and provide a workhorse for QC, association and first > stop > > visualisation. I typically use the output of these into R/ > > Bioconductor. > > That said there are some neat Bioconductor tools that you can use > > along > > side... I probably underutilise those myself , but I recommend > highly > > those "common" tools. > > > > Plink binary format for genotype data is very handy. MACH-MACH2DAT > can > > take covariates (at the end of the ped files). If is not clear what > > you > > are doing but if you have 100 cases, what are your controls ? are > you > > going to use a historical set ...WTCCC ? > > > > As for Birdseed and crlmm.To be honest I do not know if crlmm calls > > genotype AND copy number variations (like birdsuite, Birdseed is > apart > > of that), would be neat if it did. If you have expression data then > > genotypes + copy number data might be quite useful to you ..... > > depending > > on what you are studying. > > > > 100 cases is very small but I have seen success with as few as 200 > for > > some specific genetic diseases > > > > I would consider > > 1) Affymetrics own SNP calling to get genotypes + PennCNV( or > > other) to > > get copy number variations, easy and most straight forward > > OR > > Buidsuite if you feel confident (never tried it, I use Illumina) > cause > > then you get copy number variations straight away. > > > > 2) your cases + historical controls do a mini GWAS > > combine genotypes and QC with plink / eigenstrat for SAMPLES and > SNPS > > ie: > > > > SAMPLES check:(stratification, related > > individuals,missingness,heterozygosity... look for outliers ) > > > > SNPS:(MAF , genotyping rate, HWE all need to be filtered on) > > > > 3) do straight up affy micro array analysis and check against your > > mini > > GWAS > > > > 4) Really combine expression and genotypes; Try GGtools > (Bioconductor) > > on you genotypes + expression data > > OR use plink or MACH2DAT with the expression data as covariates, > > maybe. > > Plink has an excellent manual check that out. > > > > Note GGtools will not require that you do the mini GWAS as you will > > only need the cases genotypes I think see that package for details, > > but > > still do filtering before you begin. > > > > my 2c worth of ideas.... > > > > Cheers > > Paul > > > > > > > > > > > > > > > > > > > > > > > > > > -----Original Message----- > > From: Peter Ganske <peterganske at="" mac.com=""> > > To: Claus-J?rgen Scholz <scholz at="" klin-biochem.uni-wuerzburg.de=""> > > Cc: bioconductor at stat.math.ethz.ch > > Subject: Re: [BioC] SNP Analysis > > Date: Thu, 22 Oct 2009 14:51:52 +0200 > > > > Dear Claus- J?rgen, > > thanks for the reply. In which way you would analyze the genotype > > frequency wit PLINK? > > And why you use this program instead of any bioconductor- package? > > All the best and thanks in advance > > Peter > > > > > > > > Am 22.10.2009 um 13:13 schrieb Claus-J?rgen Scholz: > > > >> > >> Dear Peter, > >> > >> indeed, Birdseed is a genotyping algorithm and I'd use it for > >> genotype > >> calling of SNP6.0 arrays (best suited for this platform). If you > have > >> the calls, export them into a table (export options and formats > >> should > >> be described in the Genotyping Console manual) and analyze the > >> genotype > >> frequency differences between responders and non-responders > (valuable > >> free software is e.g. PLINK). However, n=100 is a pretty small > sample > >> size for a GWAS... > >> > >> Bests, > >> Claus-J?rgen > >> > >> > >> Peter Ganske schrieb: > >>> Dear Vincent, > >>> thanks for the fast replay. Well, i thought, that the Genotyping > >>> console used the Birdseed Algorithm and this algorithm is an > >>> Genotyping Algorithm. > >>> > >>> Its hard to find paper or groups, who worked with this array and > for > >>> me ( i work as a student for an institue) is hard to find the > right > >>> workflow without help (nobody worked here with SNP arrays in the > >>> past) > >>> > >>> So, i have 100 Arrays (100 CHP and 100 CEL files) of 100 > >>> patients. I > >>> want to have a look at the SNPs of the patients. 50 are non- > >>> responder > >>> and 50 are responder. There should be a difference between the two > >>> groups. Since yet, i looked for any papers for getting an > "general" > >>> workflow for sorting out most of the SNPs of the patients. > >>> > >>> So you think i have to try this package and create the genotyping > >>> calls? > >>> Whats about this workflow? So are my following thought right: > >>> > >>> - The package check every SNP for every Chips and put the result > >>> in a > >>> table > >>> - i can combine the result of the SNPs with a selection of gene i > >>> want.... > >>> > >>> My boss talked about a top-list of 50 genes... Maybe this can help > >>> me > >>> out for the usage of CRLMM.. dont know > >>> > >>> Thanks a lot and sorry for the questions. First time for me to > work > >>> with SNP Arrays and the first time to work with Bioconductor/R > >>> All the best from Germany > >>> Peter > >>> Am 21.10.2009 um 16:11 schrieb Vincent Carey: > >>> > >>> > >>>> Briefly, you can perform genotype calling with a confidence > measure > >>>> using crlmm package, working from the CEL files. The crlmm > >>>> package > >>>> includes a vignette called crlmmDownstream.pdf that illustrates > one > >>>> approach to GWAS analysis based on 6.0, using snpMatrix package. > >>>> To > >>>> use crlmm you will also need a metadata package called > >>>> genomewidesnp6crlmm. > >>>> > >>>> There are certainly other approaches possible. Our workflow > >>>> documentation for this use case probably needs some enhancement. > >>>> > >>>> On Wed, Oct 21, 2009 at 9:42 AM, Peter Ganske <peter.ganske at="" hki-jena.de=""> >>>> > >>>>> wrote: > >>>>> > >>>>> Hello, > >>>>> first time for me to work with SNP arrays. I got CEL- and CHP- > >>>>> files > >>>>> for my Analysis. The CEL are from Affymetrix Human-Wide Genome > >>>>> SNP- > >>>>> Array 6.0 and the CHP- files are dealed with the Birdseed- > >>>>> Algorithm (part of the Genotyp Console from Affymetrix as well). > >>>>> Is there anybody here, who worked with this arrays in the > past? I > >>>>> am looking for an (general) workflow for my study. I want to > >>>>> analyse patients with Rheumatoid Arthritis with regard to SNPs > and > >>>>> the question "why there are respoonder and non-responder for the > >>>>> therapy"? > >>>>> I am looking for an workflow for the arrays. Is it better to > work > >>>>> with the CHP files or with the CEL- files? > >>>>> Would me great, if anybody can help me out. > >>>>> Thanks in advance > >>>>> Peter > >>>>> > >>>>> > >>>>> The information contained in this email and any attachments is > >>>>> confidential and may be subject to copyright or other > intellectual > >>>>> property protection. If you are not the intended recipient, you > >>>>> are > >>>>> not authorized to use or disclose this information, and we > request > >>>>> that you notify us by reply mail or telephone and delete the > >>>>> original message from your mail system. > >>>>> [[alternative HTML version deleted]] > >>>>> > >>>>> _______________________________________________ > >>>>> 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 > >>>>> > >>>>> > >>>> The information contained in this email and any attachments is > >>>> confidential and may be subject to copyright or other > intellectual > >>>> property protection. If you are not the intended recipient, you > are > >>>> not authorized to use or disclose this information, and we > request > >>>> that you notify us by reply mail or telephone and delete the > >>>> original message from your mail system. > >>>> > >>>> The information contained in this email and any attachments is > >>>> confidential and may be subject to copyright or other > intellectual > >>>> property protection. If you are not the intended recipient, you > are > >>>> not authorized to use or disclose this information, and we > request > >>>> that you notify us by reply mail or telephone and delete the > >>>> original message from your mail system. > >>>> > >>> > >>> > >>> [[alternative HTML version deleted]] > >>> > >>> _______________________________________________ > >>> 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 > >>> > >> > >> _______________________________________________ > >> 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 > >> > >> The information contained in this email and any attachments is > >> confidential and may be subject to copyright or other intellectual > >> property protection. If you are not the intended recipient, you are > >> not authorized to use or disclose this information, and we request > >> that you notify us by reply mail or telephone and delete the > >> original message from your mail system. > > > > _______________________________________________ > > 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 > > -- > > Dr Paul Leo > > Bioinformatician > > Diamantina Institute for Cancer, Immunology and Metabolic Medicine > > University of Queensland > > > -------------------------------------------------------------------- ------------------ > > Research Wing, Bldg 1 > > Princess Alexandria Hospital > > Woolloongabba, QLD, 4102 > > Tel: +61 7 3240 7740 Mob: 041 303 8691 Fax: +61 7 3240 5946 > > Email: p.leo at uq.edu.au Web: http://www.di.uq.edu.au > > > > _______________________________________________ > > 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 > > -- > Dr Paul Leo > Bioinformatician > Diamantina Institute for Cancer, Immunology and Metabolic Medicine > University of Queensland > -------------------------------------------------------------------- ------------------ > Research Wing, Bldg 1 > Princess Alexandria Hospital > Woolloongabba, QLD, 4102 > Tel: +61 7 3240 7740 Mob: 041 303 8691 Fax: +61 7 3240 5946 > Email: p.leo at uq.edu.au Web: http://www.di.uq.edu.au > > _______________________________________________ > 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 > The information contained in this email and any attachments is > confidential and may be subject to copyright or other intellectual > property protection. If you are not the intended recipient, you are > not authorized to use or disclose this information, and we request > that you notify us by reply mail or telephone and delete the > original message from your mail system.
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@claus-jurgen-scholz-3117
Last seen 10.2 years ago
Dear Peter, PLINK is simply a convenient implementation of analysis tasks usually performed in association studies. If that's not enough, further processing of PLINK output is easily done with R - it's designed for that purpose. PLINK is actually standard software, it's freely available and also well documented on the website (http://pngu.mgh.harvard.edu/~purcell/plink/) therefore it might be worth having at look at it. If you prefer R/Bioconductor, there are the Packages GeneticsBase, SimHap (my personal favourite), GenABEL, SNPassoc... Bests, Claus-J?rgen >>> Peter Ganske <peterganske at="" mac.com=""> >>> Dear Claus- J?rgen, thanks for the reply. In which way you would analyze the genotype frequency wit PLINK? And why you use this program instead of any bioconductor- package? All the best and thanks in advance Peter Am 22.10.2009 um 13:13 schrieb Claus-J?rgen Scholz: > > Dear Peter, > > indeed, Birdseed is a genotyping algorithm and I'd use it for genotype > calling of SNP6.0 arrays (best suited for this platform). If you have > the calls, export them into a table (export options and formats should > be described in the Genotyping Console manual) and analyze the > genotype > frequency differences between responders and non-responders (valuable > free software is e.g. PLINK). However, n=100 is a pretty small sample > size for a GWAS... > > Bests, > Claus-J?rgen > > > Peter Ganske schrieb: >> Dear Vincent, >> thanks for the fast replay. Well, i thought, that the Genotyping >> console used the Birdseed Algorithm and this algorithm is an >> Genotyping Algorithm. >> >> Its hard to find paper or groups, who worked with this array and for >> me ( i work as a student for an institue) is hard to find the right >> workflow without help (nobody worked here with SNP arrays in the >> past) >> >> So, i have 100 Arrays (100 CHP and 100 CEL files) of 100 patients. I >> want to have a look at the SNPs of the patients. 50 are non- responder >> and 50 are responder. There should be a difference between the two >> groups. Since yet, i looked for any papers for getting an "general" >> workflow for sorting out most of the SNPs of the patients. >> >> So you think i have to try this package and create the genotyping >> calls? >> Whats about this workflow? So are my following thought right: >> >> - The package check every SNP for every Chips and put the result in a >> table >> - i can combine the result of the SNPs with a selection of gene i >> want.... >> >> My boss talked about a top-list of 50 genes... Maybe this can help me >> out for the usage of CRLMM.. dont know >> >> Thanks a lot and sorry for the questions. First time for me to work >> with SNP Arrays and the first time to work with Bioconductor/R >> All the best from Germany >> Peter >> Am 21.10.2009 um 16:11 schrieb Vincent Carey: >> >> >>> Briefly, you can perform genotype calling with a confidence measure >>> using crlmm package, working from the CEL files. The crlmm package >>> includes a vignette called crlmmDownstream.pdf that illustrates one >>> approach to GWAS analysis based on 6.0, using snpMatrix package. To >>> use crlmm you will also need a metadata package called >>> genomewidesnp6crlmm. >>> >>> There are certainly other approaches possible. Our workflow >>> documentation for this use case probably needs some enhancement. >>> >>> On Wed, Oct 21, 2009 at 9:42 AM, Peter Ganske <peter.ganske at="" hki-jena.de="">>> >>>> wrote: >>>> >>>> Hello, >>>> first time for me to work with SNP arrays. I got CEL- and CHP- files >>>> for my Analysis. The CEL are from Affymetrix Human-Wide Genome SNP- >>>> Array 6.0 and the CHP- files are dealed with the Birdseed- >>>> Algorithm (part of the Genotyp Console from Affymetrix as well). >>>> Is there anybody here, who worked with this arrays in the past? I >>>> am looking for an (general) workflow for my study. I want to >>>> analyse patients with Rheumatoid Arthritis w ith regard to SNPs and >>>> the question "why there are respo>>>> I am looking for an workflow for the arrays. Is it better to work >>>> with the CHP files or with the CEL- files? >>>> Would me great, if anybody can help me out. >>>> Thanks in advance >>>> Peter >>>> >>>> >>>> The information contained in this email and any attachments is >>>> confidential and may be subject to copyright or other intellectual >>>> property protection. If you are not the intended recipient, you are >>>> not authorized to use or disclose this information, and we request >>>> that you notify us by reply mail or telephone and delete the >>>> original message from your mail system. >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> 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 >>>> >>>> >>> The information contained in this email and any attachments is >>> confidential and may be subject to copyright or other intellectual >>> property protection. If you are not the intended recipient, you are >>> not authorized to use or disclose this information, and we request >>> that you notify us by reply mail or telephone and delete the >>> original message from your mail system. >>> >>> The information contained in this email and any attachments is >>> confidential and may be subject to copyright or other intellectual >>> property protection. If you are not the intended recipient, you are >>> not authorized to use or disclose this information, and we request >>> that you notify us by reply mail or telephone and delete the >>> original message from your mail system. >>> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 >> > > _______________________________________________ > 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 > > The information contained in this email and any attachments is > confidential and may be subject to copyright or other intellectual > property protection. If you are not the intended recipient, you are > not authorized to use or disclose this information, and we request > that you notify us by reply mail or telephone and delete the > original message from your mail system.
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