Entering edit mode
I am trying to run and compare `SCAN` function of package `SCAN.UPC` , since in the paper the authors showed superior performance to RMA method.
I have a cohort of Affymetrix HTA 2.0 arrays, save on my drive. when I run the code below
`
library(SCAN.UPC)
library(hta20hsentrezgprobe)
library(hta20hsentrezgcdf)
library(doParallel)
registerDoParallel(cores=3)
celFilePattern="E:/Arrays/workspace/CELfile/NORCEL/*.CEL"
normalized = SCAN(celFilePattern, probeSummaryPackage="hta20hsentrezgprobe", annotationPackageName = "hta20hsentrezgcdf", exonArrayTarget= "core")
`
I got error massage `
Error in { :
task 1 failed - "unable to find an inherited method for function 'kind' for signature '"environment"'"`
I can not figure out where the problem is. What should I change?
Thanks a lot
What do you get if you use the following on the last line of your code rather than what you currently have?
normalized = SCAN(celFilePattern)
Hi Stephen,
I tried your suggestion, and this time R did not throw and error, but the function ran for 15 min for 20 arrays and slowed my PC entirely. RAM consumption during the function execution was above 80% ( of 24GB RAM) all the time!
This process with affy::justRMA() takes less than a min on my PC.
Is that because of the Array type being not suitable for this function?
Best,
Hossin
SCAN is slower and uses more memory than some other methods. But it explicitly accounts for the probe sequences, thus adjusting for probe-sequence composition on a single-sample basis, unlike other methods. If speed is a concern, you can try the SCANfast function, which should give similar results and be faster.