Entering edit mode
Good Afternoon,
I am trying to do present absent calls on my Clariom chips with oligo's paCalls function, but each time I receive a subscript out of bounds error. I've tried the Human S HT and Mouse S Clariom chips. Does anyone know of a work around?
Thanks,
Kristin
Script:
library(oligo)pd<-read.AnnotatedDataFrame('Phenotype.txt', row.names = 'SampleName', header = T, sep = '\t')celfiles <- read.celfiles(filenames = c('sample1.CEL', 'sample2.CEL', 'sample3.CEL', 'sample4.CEL', 'sample5.CEL', 'sample6.CEL'), phenoData=pd)PApset <- paCalls(celfiles,"MAS5")
Error:
Getting probe level data... OK.
Error in mms[o, , drop = FALSE] : subscript out of bounds
As a followup, you should just get an error saying that paCalls doesn't work with this particular array. The ExpressionFeatureSet was originally intended for the old style 3'-biased arrays, which mostly did have MM probes (although even back then Affy was phasing them out).
When I added the Clariom S arrays to pdInfoBuilder, I used this class, because in most respects the Clariom S arrays are very similar to the old 3'-biased arrays. I'll add a more informative error message.