Dear Bioconductor, I have CEL files ONLY, no other files I have. how should I read phenodata or MAIME information from there. Do i need Phenodata.txt/MAIME.txt for Microarray analysis or make one or where can i get it? Presently I am doing: my.filenames <- list.files(,"CEL"); f <- as.matrix(my.filenames); n <- nrow(f); # to get number of files in my list make use for furthere analysis my.pheno <- read.phenoData(sampleNames = my.filenames); abatch <- ReadAffy(filenames = my.filenames,phenoData = my.pheno); I am student at University of New Haven,CT and I am doing Microarray analysis by myself. I highly appreciate your reply, Saurin Jani

You don't need either phenoData or MIAME information in order to analyze your data. These things are simply useful information that you *could* use for analysis (in the case of phenoData), or for data reporting (in the case of MIAME). Neither is strictly necessary. In fact, I personally have yet to use either. HTH, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> SAURIN <saurin_jani@yahoo.com> 06/09/04 10:27AM >>> Dear Bioconductor, I have CEL files ONLY, no other files I have. how should I read phenodata or MAIME information from there. Do i need Phenodata.txt/MAIME.txt for Microarray analysis or make one or where can i get it? Presently I am doing: my.filenames <- list.files(,"CEL"); f <- as.matrix(my.filenames); n <- nrow(f); # to get number of files in my list make use for furthere analysis my.pheno <- read.phenoData(sampleNames = my.filenames); abatch <- ReadAffy(filenames = my.filenames,phenoData = my.pheno); I am student at University of New Haven,CT and I am doing Microarray analysis by myself. I highly appreciate your reply, Saurin Jani _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

Dear bioconductor, Thank you for replying me, but, I would like to report data highly informative manner, so, I suppose I would like to use MIAME.txt file. so, please, let me know, how can I make use of MAIME.txt file or where can I get it, and ..again, I am having only CEL files. for every cel file, i would use: i hope this is right: My scripts does 1. RMA--> 2. ANOVA --->(ttest if necessary)---> (if ttest it does adjust p-value by multiple hypothesis) and 3. Extract sigenificant genes 4. report by annotation & chromosome ploting Thank you, Saurin Jani --- James MacDonald <jmacdon@med.umich.edu> wrote: > You don't need either phenoData or MIAME information in order to analyze > your data. These things are simply useful information that you *could* > use for analysis (in the case of phenoData), or for data reporting (in > the case of MIAME). Neither is strictly necessary. In fact, I personally > have yet to use either. > > HTH, > > Jim > > > > James W. MacDonald > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > > >>> SAURIN <saurin_jani@yahoo.com> 06/09/04 10:27AM >>> > Dear Bioconductor, > > I have CEL files ONLY, no other files I have. > how should I read phenodata or MAIME information from there. Do i need > Phenodata.txt/MAIME.txt for > Microarray analysis or make one or where can i get it? > > Presently I am doing: > > my.filenames <- list.files(,"CEL"); > f <- as.matrix(my.filenames); > n <- nrow(f); # to get number of files in my list make use for furthere > analysis > > my.pheno <- read.phenoData(sampleNames = my.filenames); > abatch <- ReadAffy(filenames = my.filenames,phenoData = my.pheno); > > > > I am student at University of New Haven,CT and I am doing Microarray > analysis by myself. > > > I highly appreciate your reply, > > Saurin Jani > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

If you look in the help files for both read.MIAME and read.phenoData, you will see that you can either supply a flat file for either function, or use widgets to enter the information manually. What you enter in these files are information about the experimenter, the lab, etc, (for MIAME) and phenotypic data about the samples (for phenoData). Therefore, you have to get this information from whoever is doing the experiments. HTH, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> SAURIN <saurin_jani@yahoo.com> 06/09/04 11:13AM >>> Dear bioconductor, Thank you for replying me, but, I would like to report data highly informative manner, so, I suppose I would like to use MIAME.txt file. so, please, let me know, how can I make use of MAIME.txt file or where can I get it, and ..again, I am having only CEL files. for every cel file, i would use: i hope this is right: My scripts does 1. RMA--> 2. ANOVA --->(ttest if necessary)---> (if ttest it does adjust p-value by multiple hypothesis) and 3. Extract sigenificant genes 4. report by annotation & chromosome ploting Thank you, Saurin Jani --- James MacDonald <jmacdon@med.umich.edu> wrote: > You don't need either phenoData or MIAME information in order to analyze > your data. These things are simply useful information that you *could* > use for analysis (in the case of phenoData), or for data reporting (in > the case of MIAME). Neither is strictly necessary. In fact, I personally > have yet to use either. > > HTH, > > Jim > > > > James W. MacDonald > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > > >>> SAURIN <saurin_jani@yahoo.com> 06/09/04 10:27AM >>> > Dear Bioconductor, > > I have CEL files ONLY, no other files I have. > how should I read phenodata or MAIME information from there. Do i need > Phenodata.txt/MAIME.txt for > Microarray analysis or make one or where can i get it? > > Presently I am doing: > > my.filenames <- list.files(,"CEL"); > f <- as.matrix(my.filenames); > n <- nrow(f); # to get number of files in my list make use for furthere > analysis > > my.pheno <- read.phenoData(sampleNames = my.filenames); > abatch <- ReadAffy(filenames = my.filenames,phenoData = my.pheno); > > > > I am student at University of New Haven,CT and I am doing Microarray > analysis by myself. > > > I highly appreciate your reply, > > Saurin Jani > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor __________________________________ Do you Yahoo!? Friends. Fun. Try the all-new Yahoo! Messenger. http://messenger.yahoo.com/