Dear Community,

i have tried recently to read, process and analyze some human clariom array CEL files in R-unfortunately, i have no information from my collaborators which specific platform has been used (for example S or D)-so i tried the following approach:

library(oligo)
library(affycoretools)
library(limma)
library(org.Hs.eg.db)

dat <- read.celfiles(list.celfiles())

# Platform design info loaded.
Reading in : 01_SUM-159.CEL
Reading in : 02_SUM-159-WT1.CEL
Reading in : 03_SUM-159-WT3.CEL
Reading in : 04_SUM-159-WT4.CEL
Reading in : 05_SUM-159-WT5.CEL
Reading in : 06_SUM-159-WT6.CEL
Reading in : 07_SUM-159-KO3.CEL
Reading in : 08_SUM-159-KO4.CEL
Reading in : 09_SUM-159-KO5.CEL
Reading in : 10_SUM-159-KO6.CEL
Reading in : 11_SUM-159-KO8.CEL
Reading in : 12_SUM-159-KO10.CEL

dat
GeneFeatureSet (storageMode: lockedEnvironment)
assayData: 2598544 features, 12 samples 
  element names: exprs 
protocolData
  rowNames: 01_SUM-159.CEL 02_SUM-159-WT1.CEL ...
    12_SUM-159-KO10.CEL (12 total)
  varLabels: exprs dates
  varMetadata: labelDescription channel
phenoData
  rowNames: 01_SUM-159.CEL 02_SUM-159-WT1.CEL ...
    12_SUM-159-KO10.CEL (12 total)
  varLabels: index
  varMetadata: labelDescription channel
featureData: none
experimentData: use 'experimentData(object)'
Annotation: pd.hugene.2.0.st

z <- pData(dat)

otherdat <- data.frame(Condition_Clariom = c("WT","WT","WT","WT","WT","WT",
"KO_clone","KO_clone","KO_clone","KO_clone","KO_clone","KO_clone"))

z <- data.frame(z, otherdat)
pData(dat) <- z
validObject(dat)

celfiles.rma <- rma(dat, target="core")
eset.rma <- getMainProbes(celfiles.rma)

# library(hugene20sttranscriptcluster.db)
eset.rma <- annotateEset(eset.rma, hugene20sttranscriptcluster.db).....

Thus, my main question is: as above after reading the raw CEL files, the annotation platform of the dat object is pd.hugene.2.0.st, could i use the above procedure with hugene20sttranscriptcluster.db as annotation ?

Or my above approach is incorrect and i should use another annotation R package ?

Thank you in advance,

Efstathios

That's the conventional thing to do. Why do you have doubts? Also, why do you think these are clariom arrays?