[BioC] Problems highlight control spots in MA plots
christian.riedel at biologie.uni-ulm.de
christian.riedel at biologie.uni-ulm.de
Sun Nov 23 18:34:24 MET 2003
Hello,
In our Lab we are starting to run microarray analysis by using the mArray
package. We followed the 'Biologists guide to using Bioconductor' published Nov
2002 by C. Bye:
http://www.people.fas.harvard.edu/~grosu/downloads/bioconductor_manual.pdf
Following the instructions we modified the gal file introducing a
column "controls" to specify the blanks and N/A spots. To vizualize these
controls in MA plots we try this R code (as indicated in the guide):
blanks<-maText(subset=maControls(christian.raw[,1]) == "EMPTY") , labels="o",
col="purple")
maPlot(christian.raw[,1], text.func = blanks)
We tried to exchange "EMPTY" by any control specified and even tried "Control"
In any case this resulted in a "syntax error"
We crosschecked whether these controls are accesible with the following code:
maImage(christian.raw[,1], x="maControls)
There we get a warning message and no plot.
Here is an extract of our modified gal file. To our knowledge this should be ok.
Block Row Column ID Name Controls
4 21 5 H200021155 Homo sapiens cDNA FLJ30327
fis OK
4 21 7 H200021179 Homo sapiens cDNA FLJ32985
fi OK
4 21 8 H200021185 Homo sapiens cDNA FLJ30893
fis OK
4 21 9 n/a n/a NA
4 21 16 n/a n/a NA
4 22 3 Blank Blank EMPTY
4 22 5 Blank Blank EMPTY
Does anybody know how to handle this operation (visualization of control spots
specified in the gal file) or if we made some other mistake?
Thanks (in advance) for help,
Christian Riedel
Ph.D. student
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