[BioC] Regarding Phenodata and MAIME data
saurin_jani at yahoo.com
Wed Jun 9 17:13:00 CEST 2004
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
--- James MacDonald <jmacdon at 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.
> James W. MacDonald
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> >>> SAURIN <saurin_jani at 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
> 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 at stat.math.ethz.ch
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