Question: duplicateCorrelation question
gravatar for Scott Ochsner
10.8 years ago by
Scott Ochsner300
Scott Ochsner300 wrote:
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) i386-pc-mingw32 locale: 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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