[BioC] marrayNorm - Getting Data Out

[Jean Yee Hwa Yang]

Hi Michael,

There is method maGeneTable that will do that for you.
write.table(cbind(maGeneTable(data), maM(data)), file="data.txt")

Cheers

Jean

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 Jean Yee Hwa Yang			 jean at biostat.ucsf.edu
 Division of Biostatistics,		   Tel: (415) 476-3368
 University of California,		   Fax: (415) 476-6014
 500 Parnassus Avenue, MU 420-W,  San Francisco, CA 94143-0560
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

On Tue, 5 Aug 2003, michael watson (IAH-C) wrote:

> OK, just to answer my own dumb question, it's something along the lines of:
> 
> write.table(cbind(maGridRow(lowess.norm), maGridCol(lowess.norm),
> maSpotCol(lowess.norm), maSpotRow(lowess.norm), maM(lowess.norm)),
> file="C:\\test.txt")
> 
> This will output grid location along with normalised M values for the
> marrayNorm object lowess.norm.  If I have Gene Names in there, I can
> add maGnames(lowess.norm) to my list in the call to cbind()
> 
> Thanks for your patience :-D
> 
> 
> -----Original Message-----
> From: michael watson (IAH-C) 
> Sent: 05 August 2003 11:21
> To: 'James MacDonald'; michael watson (IAH-C);
> bioconductor at stat.math.ethz.ch
> Subject: RE: [BioC] marrayNorm - Getting Data Out
> 
> 
> Great :-)
> 
> I can use write.table() to get my normalised M values out into a tab delimited text file, but how do I also output the the spot annotations which I read in from my GAL file?
> 
> Do I:
> 
> - output my normalised M values using write.table()
> - output my spot annotations using maGnames(data) and write.table()
> - paste the two together in Excel or link them in Access?
> 
> I can of course do the above, I just wondered if there was an output function that would basically output all of my normalised log ratios alongside all the spot annotations I read in to my marrayInfo object.
> 
> Thanks
> Mick
> 
> -----Original Message-----
> From: James MacDonald [mailto:jmacdon at med.umich.edu]
> Sent: 03 August 2003 04:37
> To: michael.watson at bbsrc.ac.uk; bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] marrayNorm - Getting Data Out
> 
> 
> If you want your normalized log ratios, you can get them out of the
> marrayNorm object using the accessor function maM. For instance, if your
> marrayNorm object was called mydata, you would do something like:
> 
> ratios <- maM(mydata)
> then write.table(ratios, ...)
> 
> for more info, try ?marrayNorm
> 
> 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
> 
> >>> "michael watson (IAH-C)" <michael.watson at bbsrc.ac.uk> 07/31/03
> 06:16AM >>>
> Hi
> 
> This sounds kind of stupid, but if I have my data in an marrayNorm
> object, can anyone give any pointers on how to get it out into, say, a
> tab-delimited text file?  
> 
> Are there any special functions or is it simply write.table() ..??
> 
> Thanks
> Mick
> 
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