[BioC] probeset level visualization with standard deviation...

Paul Hammer hammer_p at molgen.mpg.de
Wed Feb 20 18:12:35 CET 2008

hi members,

i am looking for a function which plots me average probeset levels with 
standard deviations (e.g. tissues 1 against tissue 2). Is there any 
functions which could do this. i work with affymetrix chips which have 
often three times determination.

an example for a better understanding:

after using the functions read.exon() and rma() i specify my probeset_ids:

 > probeset = gene.to.probeset("ensemle_gene_id")
 > exon_probesets = select.probewise(probeset, filter="exonic")

now i would like to have the average values with the standard deviation 
for these probeset_id log levels to plot e.g. two tissues (here heart 
and breast) against later.

probeset_id    heart_A.CEL       heart_B.CEL    heart_C.CEL     
breast_A.CEL    breast_B.CEL    breast_C.CEL
1.                   6.5432                6.7833              6.3234   
            4.6566               5.2121               4.7654
2.                   5.8422                6.0813              6.2334   
            5.2526               5.1236               4.9234
3.                   5.8422                6.0813              6.2334   
            5.2526               5.1236               4.9234

is there any simple way? till now i extract all data from a data.frame 
given by splicing.index(), calculate average and sd for every 
probeset_id and tissue, which is quite complicated.


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