[BioC] marrayNorm - Getting Data Out

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Tue Aug 5 15:44:35 MEST 2003

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.


-----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



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

>>> "michael watson (IAH-C)" <michael.watson at bbsrc.ac.uk> 07/31/03
06:16AM >>>

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() ..??


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