How to use detect call in GCRMA (or RMA) analysis?

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Wang mingyi ▴ 10

@wang-mingyi-1965

Last seen 10.2 years ago

Dear all, I have a question for Affymetrix data analysis by GCRMA (or RMA). From the GCRMA (RMA) results, we cannot get detect call information which can be returned from MAS5. I think this information are useful when we want to perform some downstream t-tests. For example, three replicates (after drug) comparing with other three replicates (before drug), if given one gene, most detect values are "A" in all these 6 replicates, we will think the t-test doesnot make sense. So how to deal with this situation? Can we incorporate with detect call information from MAS5? Thank you in advance! _________________________________________________________________ ?????????????????????????????? MSN Hotmail?? http://www.hotmail.com

gcrma gcrma • 1.4k views

ADD COMMENT • link updated 18.0 years ago by Jianping Jin ▴ 890 • written 18.0 years ago by Wang mingyi ▴ 10

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Kasper Daniel Hansen ★ 6.5k

@kasper-daniel-hansen-2979

Last seen 17 months ago

United States

On Dec 6, 2006, at 2:47 PM, Wang mingyi wrote: > Dear all, > > I have a question for Affymetrix data analysis by GCRMA (or RMA). > From the GCRMA (RMA) results, we cannot get detect call information > which can be returned from MAS5. I think this information are > useful when we want to perform some downstream t-tests. For > example, three replicates (after drug) comparing with other three > replicates (before drug), if given one gene, most detect values are > "A" in all these 6 replicates, we will think the t-test doesnot > make sense. So how to deal with this situation? Can we incorporate > with detect call information from MAS5? > Thank you in advance! GCRMA or RMA does not make presence/absence calls like MAS5 does. One way to deal with this is to do the relevant routine and then subsequently remove the probesets which are declared absent using MAS5. You could also remove them before doing RMA/GCRMA but that is a bit harder. Kasper > _________________________________________________________________ > ??????????????? MSN Hotmail? http:// > www.hotmail.com > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor

ADD COMMENT • link 18.0 years ago Kasper Daniel Hansen ★ 6.5k

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Jianping Jin ▴ 890

@jianping-jin-1212

Last seen 10.2 years ago

You may want to try "mas5calls", a function in the affy package and then filter out the probesets with most absent calls. For example: PAcalls <- mas5calls(affybatch.obj) HTH, JP- --On Wednesday, December 06, 2006 10:47 PM +0000 Wang mingyi <mingyiwang at="" hotmail.com=""> wrote: > Dear all, > > I have a question for Affymetrix data analysis by GCRMA (or RMA). From > the GCRMA (RMA) results, we cannot get detect call information which can > be returned from MAS5. I think this information are useful when we want > to perform some downstream t-tests. For example, three replicates (after > drug) comparing with other three replicates (before drug), if given one > gene, most detect values are "A" in all these 6 replicates, we will think > the t-test doesnot make sense. So how to deal with this situation? Can we > incorporate with detect call information from MAS5? > Thank you in advance! > > _________________________________________________________________ > ??????????????? MSN Hotmail? > http://www.hotmail.com > ################################## Jianping Jin Ph.D. Bioinformatics scientist Center for Bioinformatics Room 3133 Bioinformatics building CB# 7104 University of Chapel Hill Chapel Hill, NC 27599 Phone: (919)843-6105 FAX: (919)843-3103 E-Mail: jjin at email.unc.edu

ADD COMMENT • link 18.0 years ago Jianping Jin ▴ 890

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If you have a PM-only array, the mas5calls function will not do. I've seen a couple of ad hoc strategies for calling P/A only from PM probes, but never accompanied with comparison to MAS5 or some other quality metric. Has anyone dealt with this problem? -Amit On Dec 7, 2006, at 8:21 AM, Jianping Jin wrote: > You may want to try "mas5calls", a function in the affy package and > then > filter out the probesets with most absent calls. > For example: > > PAcalls <- mas5calls(affybatch.obj) > > HTH, > > JP- > > --On Wednesday, December 06, 2006 10:47 PM +0000 Wang mingyi > <mingyiwang at="" hotmail.com=""> wrote: > >> Dear all, >> >> I have a question for Affymetrix data analysis by GCRMA (or RMA). >> From >> the GCRMA (RMA) results, we cannot get detect call information >> which can >> be returned from MAS5. I think this information are useful when we >> want >> to perform some downstream t-tests. For example, three replicates >> (after >> drug) comparing with other three replicates (before drug), if >> given one >> gene, most detect values are "A" in all these 6 replicates, we >> will think >> the t-test doesnot make sense. So how to deal with this situation? >> Can we >> incorporate with detect call information from MAS5? >> Thank you in advance! >> >> _________________________________________________________________ >> ??????????????? MSN Hotmail? >> http://www.hotmail.com >> > > > > ################################## > Jianping Jin Ph.D. > Bioinformatics scientist > Center for Bioinformatics > Room 3133 Bioinformatics building > CB# 7104 > University of Chapel Hill > Chapel Hill, NC 27599 > Phone: (919)843-6105 > FAX: (919)843-3103 > E-Mail: jjin at email.unc.edu > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor

ADD REPLY • link 18.0 years ago Amit Bahl ▴ 20

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