Hi all, I used functions of pairwise.filter and results.summary from simpleaffy package to do gene filtering and summarization: results <- pairwise.comparison(eset, var1,c(group1,group2), spots = data_cel) g_inten7 <- pairwise.filter(results,min.exp=1,min.exp.no=0,min.present.no=0,presen t.by.group=F,fc=0,tt=1);#trying to keep all genes summary_filtered <- results.summary(g_inten7,"hgu133a") But, I got following error: > Getting probe level data... Computing p-values Doing PMA Calls Error: value for 'AFFX-r2-Hs18SrRNA-5_at' not found When I checked 'AFFX-r2-Hs18SrRNA-5_at' in g_inten7 I did see a value in 'AFFX-r2-Hs18SrRNA-5_at'. I'm not sure if this error is associated with hgu133a and hgu133acdf or simpleaffy package. Your help will be highly appreciated. Jack Zhu, MD, MS Lombardi Cancer center Georgetown University 3970 Reservoir Rd, NW, NRB, W405b Washington, DC 20057 Email: yz8 at georgetwon.edu Tel: (202)-687-7451 Web: http://clarkelabs.georgetown.edu

Hi Crispin, Thank you for your reply. results <- pairwise.comparison(eset, var1,c(group1,group2), spots = data_cel) where: var1: column in pData(x) c(group1,group2): labels in group Jack ----- Original Message ----- From: "Crispin Miller" <cmiller@picr.man.ac.uk> To: "Jack Zhu" <yz8 at="" georgetown.edu="">; <bioconductor at="" stat.math.ethz.ch=""> Sent: Tuesday, June 28, 2005 5:25 AM Subject: RE: [BioC] error with results.summary in simpleaffy Hi, What are var1, group1 and group2 in your example? Crispin -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Jack Zhu Sent: 27 June 2005 19:13 To: bioconductor at stat.math.ethz.ch Subject: [BioC] error with results.summary in simpleaffy Hi all, I used functions of pairwise.filter and results.summary from simpleaffy package to do gene filtering and summarization: results <- pairwise.comparison(eset, var1,c(group1,group2), spots = data_cel) g_inten7 <- pairwise.filter(results,min.exp=1,min.exp.no=0,min.present.no=0,presen t. by.group=F,fc=0,tt=1);#trying to keep all genes summary_filtered <- results.summary(g_inten7,"hgu133a") But, I got following error: > Getting probe level data... Computing p-values Doing PMA Calls Error: value for 'AFFX-r2-Hs18SrRNA-5_at' not found When I checked 'AFFX-r2-Hs18SrRNA-5_at' in g_inten7 I did see a value in 'AFFX-r2-Hs18SrRNA-5_at'. I'm not sure if this error is associated with hgu133a and hgu133acdf or simpleaffy package. Your help will be highly appreciated. Jack Zhu, MD, MS Lombardi Cancer center Georgetown University 3970 Reservoir Rd, NW, NRB, W405b Washington, DC 20057 Email: yz8 at georgetwon.edu Tel: (202)-687-7451 Web: http://clarkelabs.georgetown.edu _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}

Hi, What are var1, group1 and group2 in your example? Crispin -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Jack Zhu Sent: 27 June 2005 19:13 To: bioconductor at stat.math.ethz.ch Subject: [BioC] error with results.summary in simpleaffy Hi all, I used functions of pairwise.filter and results.summary from simpleaffy package to do gene filtering and summarization: results <- pairwise.comparison(eset, var1,c(group1,group2), spots = data_cel) g_inten7 <- pairwise.filter(results,min.exp=1,min.exp.no=0,min.present.no=0,presen t. by.group=F,fc=0,tt=1);#trying to keep all genes summary_filtered <- results.summary(g_inten7,"hgu133a") But, I got following error: > Getting probe level data... Computing p-values Doing PMA Calls Error: value for 'AFFX-r2-Hs18SrRNA-5_at' not found When I checked 'AFFX-r2-Hs18SrRNA-5_at' in g_inten7 I did see a value in 'AFFX-r2-Hs18SrRNA-5_at'. I'm not sure if this error is associated with hgu133a and hgu133acdf or simpleaffy package. Your help will be highly appreciated. Jack Zhu, MD, MS Lombardi Cancer center Georgetown University 3970 Reservoir Rd, NW, NRB, W405b Washington, DC 20057 Email: yz8 at georgetwon.edu Tel: (202)-687-7451 Web: http://clarkelabs.georgetown.edu _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}