Dear all,

 

(my sessionInfo() is pasted at the end of this mail for those who are interested)

 

I have a MAList object which contains normalized data of two agilent ChIP on Chip arrays. When I plot the densities with plotDensities() I see one big nice peek at a level of about 9 which I think is the data I want to look at. However, there is also some "noise" at intensities below 5 or even below 0. Is there a way to exclude those spots from my further analysis? If one could plot the densities I guess one should in principle be able to access them in the MAList object but I did not find a way how to do so?!

 

Thanks for any help,

 

Torsten

 

 

> sessionInfo()

R version 2.9.1 (2009-06-26) 

i386-pc-mingw32 

 

locale:

LC_COLLATE=Norwegian (Bokmål)_Norway.1252;LC_CTYPE=Norwegian (Bokmål)_Norway.1252;LC_MONETARY=Norwegian (Bokmål)_Norway.1252;LC_NUMERIC=C;LC_TIME=Norwegian (Bokmål)_Norway.1252

 

attached base packages:

[1] stats     graphics  grDevices datasets  utils     methods   base     

 

other attached packages:

[1] limma_2.18.2  Biobase_2.4.1

 

loaded via a namespace (and not attached):

 [1] annotate_1.22.0     AnnotationDbi_1.6.1 DBI_0.2-4          

 [4] genefilter_1.24.2   grid_2.9.1          lattice_0.17-25    

 [7] Matrix_0.999375-29  Ringo_1.9.5         RSQLite_0.7-1      

[10] splines_2.9.1       survival_2.35-4     tools_2.9.1        

[13] xtable_1.5-5       

 

Torsten Waldminghaus

Department of Cell Biology

Institute for Cancer Research

Rikshospitalet-Radiumhospitalet-HF

Ullernchaussen 70

0310 Oslo

tel: 47-22935973

fax: 47-22934580

e-mail: Torsten.Waldminghaus@rr-research.no

http://openwetware.org/wiki/User:Torsten_Waldminghaus

 


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