Question: paCalls with Clariom Chips
0
gravatar for kmvaldez2
2.2 years ago by
kmvaldez20
United States / Bethesda, MD / National Institutes of Health
kmvaldez20 wrote:

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

      

microarray oligo clariom • 386 views
ADD COMMENTlink modified 2.2 years ago by James W. MacDonald51k • written 2.2 years ago by kmvaldez20
Answer: paCalls with Clariom Chips
1
gravatar for James W. MacDonald
2.2 years ago by
United States
James W. MacDonald51k wrote:

You can't do a MAS5 style P/A call with an array that has no MM probes.

ADD COMMENTlink written 2.2 years ago by James W. MacDonald51k
1

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.

ADD REPLYlink written 2.2 years ago by James W. MacDonald51k
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