paCalls with Clariom Chips
1
0
Entering edit mode
kmvaldez2 • 0
@kmvaldez2-13554
Last seen 4.1 years ago
United States / Bethesda, MD / National…

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

      

oligo microarray clariom • 626 views
ADD COMMENT
1
Entering edit mode
@james-w-macdonald-5106
Last seen 3 hours ago
United States

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

ADD COMMENT
1
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 244 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6