Detection call for Hu6800
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Claire Wilson ▴ 280
@claire-wilson-273
Last seen 7.3 years ago
Hi Christian, This error arises because simpleaffy doesn't know what the alpha1 and alpha2 values are for the Hu6800 chips and you need to supply them with the call to detection.p.val pv17 <- detection.p.val(M17, alpha1=X,alpha2=Y) Hope this helps Claire > -----Original Message----- > From: bioconductor-bounces@stat.math.ethz.ch > [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of > Christian.Stratowa@vie.boehringer-ingelheim.com > Sent: 30 March 2005 09:08 > To: bioconductor@stat.math.ethz.ch > Subject: [BioC] Detection call for Hu6800 > > Dear BioC people > > Could it be that neither detection.p.value (simpleaffy) nor > mas5calls (affy) > work with Hu6800 chips? > > I get the following errors: > > > M17 <- ReadAffy(filenames=c("M17.cel")) > > dpv17 <- detection.p.val(M17) > Error in if (alpha1 < 0) { : missing value where TRUE/FALSE needed > > dpv17 <- mas5calls(M17) > Getting probe level data... > Computing p-values > Making P/M/A Calls > Error in if (y < alpha1) { : missing value where TRUE/FALSE needed > > dpv17 <- mas5calls(M17,ignore.saturated=F) > Getting probe level data... > Computing p-values > Making P/M/A Calls > Error in if (y < alpha1) { : missing value where TRUE/FALSE needed > > > > Best regards > Christian Stratowa > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}
hu6800 probe simpleaffy hu6800 probe simpleaffy • 606 views
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@christianstratowavieboehringer-ingelheimcom-545
Last seen 7.3 years ago
Dear Clair Thank you for this information, now it works fine. BTW, I have also contacted Crispin Miller, who promised to add the missing information for Hu6800. Best regards Christian -----Original Message----- From: Claire Wilson [mailto:ClaireWilson@PICR.man.ac.uk] Sent: Friday, April 01, 2005 11:04 To: Christian.Stratowa@vie.boehringer-ingelheim.com Cc: bioconductor@stat.math.ethz.ch Subject: RE: [BioC] Detection call for Hu6800 Hi Christian, This error arises because simpleaffy doesn't know what the alpha1 and alpha2 values are for the Hu6800 chips and you need to supply them with the call to detection.p.val pv17 <- detection.p.val(M17, alpha1=X,alpha2=Y) Hope this helps Claire > -----Original Message----- > From: bioconductor-bounces@stat.math.ethz.ch > [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of > Christian.Stratowa@vie.boehringer-ingelheim.com > Sent: 30 March 2005 09:08 > To: bioconductor@stat.math.ethz.ch > Subject: [BioC] Detection call for Hu6800 > > Dear BioC people > > Could it be that neither detection.p.value (simpleaffy) nor > mas5calls (affy) > work with Hu6800 chips? > > I get the following errors: > > > M17 <- ReadAffy(filenames=c("M17.cel")) > > dpv17 <- detection.p.val(M17) > Error in if (alpha1 < 0) { : missing value where TRUE/FALSE needed > > dpv17 <- mas5calls(M17) > Getting probe level data... > Computing p-values > Making P/M/A Calls > Error in if (y < alpha1) { : missing value where TRUE/FALSE needed > > dpv17 <- mas5calls(M17,ignore.saturated=F) > Getting probe level data... > Computing p-values > Making P/M/A Calls > Error in if (y < alpha1) { : missing value where TRUE/FALSE needed > > > > Best regards > Christian Stratowa > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}

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