Search
Question: paCalls with Clariom Chips
0
gravatar for kmvaldez2
3 months ago by
kmvaldez20
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

      

ADD COMMENTlink modified 3 months ago by James W. MacDonald45k • written 3 months ago by kmvaldez20
0
gravatar for James W. MacDonald
3 months ago by
United States
James W. MacDonald45k wrote:

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

ADD COMMENTlink written 3 months ago by James W. MacDonald45k

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 3 months ago by James W. MacDonald45k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 138 users visited in the last hour