[BioC] duplicateCorrelation question

Ochsner, Scott A sochsner at bcm.tmc.edu
Mon Jan 12 19:23:02 CET 2009

Dear list,

I have an array with duplicate spots that are not evenly spaced.  The help for duplicateCorrelation indicates that the spots should be spaced evenly and designated using the spacing argument.  I'm wondering if I can order the rows of my MAlist such that the duplicate spots are on evenly spaced rows
and then run duplicate correlation.  What I have done is below.  Is reordering O.K.?  Does duplicateCorrelation use the print setup in a way in which reordering the rows is not a good idea?

#prior to reordering my MAlist
> dim(MAlist)
[1] 13284    16
> corfit <- duplicateCorrelation(MAlist,design,ndups=2,spacing=554)
Error in dim(M) <- c(spacing, ndups, ngroups, nslides) : 
  dims [product 195008] do not match the length of object [212544]

#close inspection at this point reveals that some of the spots were not evenly spaced
#I then reordered the Malist according to Malist$genes$Name slot
> MAlist2<-MAlist[order(MAlist$genes$Name),]
> corfit <- duplicateCorrelation(MAlist2,design,ndups=2,spacing=1)
> corfit$consensus.correlation
[1] 0.8968798

> sessionInfo()
R version 2.8.0 (2008-10-20) 

LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] statmod_1.3.8 Biobase_2.2.0 limma_2.16.2   

Scott A. Ochsner, Ph.D.
NURSA Bioinformatics
Molecular and Cellular Biology
Baylor College of Medicine
Houston, TX. 77030
phone: 713-798-6227 

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