Question: Correct annotation R package for human clariom array analysis
0
gravatar for svlachavas
9 months ago by
svlachavas740
Greece/Athens/National Hellenic Research Foundation
svlachavas740 wrote:

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

ADD COMMENTlink modified 9 months ago by James W. MacDonald52k • written 9 months ago by svlachavas740
Answer: Correct annotation R package for human clariom array analysis
1
gravatar for James W. MacDonald
9 months ago by
United States
James W. MacDonald52k wrote:

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

ADD COMMENTlink written 9 months ago by James W. MacDonald52k

Dear James,

thanks for your reply-unfortunately, i have just an excel file-which has an extra description for these cel files with the abbreviation "Clariom_SUM159"-where SUM159 is a cancer cell line-and i can't currently have any other extra information-

thus, you believe that perhaps these are not even clariom and are indeed gene st arrays ? my initial doubt for the analysis was because i have never analyzed in the past clariom arrays (if indeed these are...)

ADD REPLYlink written 9 months ago by svlachavas740

Wait. You show a bunch of code that makes it look like you have celfiles that you read in and processed using oligo, but now you say you just have an Excel spreadsheet? Why would you post a bunch of code that has no relation to what you are actually doing?

ADD REPLYlink written 9 months ago by James W. MacDonald52k

Dear James, please excuse me for any unintended misunderstanding- indeed these are the relative CEL files for the experiment-i just meant that any information about the experiment, is on an extra excel file, that only mentions the above information-

ADD REPLYlink written 9 months ago by svlachavas740

If the oligo package says they are hugene20 arrays, then you can be assured that is what they are.

ADD REPLYlink written 9 months ago by James W. MacDonald52k
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