[BioC] Regarding Phenodata and MAIME data

[James MacDonald]

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 at 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 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.
> 
> 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 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
> 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
> 
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