Question: reading CELfiles for Human Exon 1.0 ST Array [CDF: HuEx-1_0-st-v2,coreR3,A20071112,EP]
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gravatar for 12021560-002
2.9 years ago by
12021560-00210
12021560-00210 wrote:

Hi I am reading microarray data (CEL files) through R. While reading GSE35021 based on platform Affymetrix Human Exon 1.0 ST Array [CDF: HuEx-1_0-st-v2,coreR3,A20071112,EP] I am getting this error when i give command to read these files. let me clear I am using oligo pkg to read celfiles for this platform. Could please help how to remove this error? Is there is some other pkg to read files for this package? if yes then kindly share the name of pkg and command as well.

rawData <- read.celfiles(celfiles)   
Error in read.celfiles.header (x):
Is GSE35021/CEL/GPL9793_gene_assignment
ADD COMMENTlink modified 2.9 years ago by genomax65k • written 2.9 years ago by 12021560-00210

Your GSE35021/CEL/GPL9793_gene_assignment is not a CEL file. It should end by .CEL or .CEL.gz

ADD REPLYlink written 2.9 years ago by Ar830

this is the script I am using. Am i giving write commands please pick up the error

library(affy)

library(limma)

library(annotate)

library(oligo)

library("pd.huex.1.0.st.v2")

library("huex10sttranscriptcluster.db")

gse30521dat = getGEO('GSE30521')

gse30521raw= getGEOSuppFiles("GSE30521")

tarfile<- grep(".tar$", rownames(gse30521raw), value = TRUE)

list.files("GSE30521")

untar("GSE30521/GSE30521_RAW.tar", exdir = "GSE30521/CEL")

list.files("GSE30521/CEL")

celfiles<- list.files("GSE30521/CEL", full = TRUE)

rawData<- read.celfiles(celfiles)

ADD REPLYlink written 2.9 years ago by 12021560-00210

Sometimes you need to see/read the error properly. Apart from *.CEL.gz files, your folder has 3 more files:

  1. GPL9793_gene_assignments.txt.gz
  2. GPL9793_HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf.gz
  3. GPL9793_HuEx-1_0-st-v2.na26.hg18.transcript.csv.gz

Either move them to other folder or do

> rawData <- read.celfiles(celfiles[4:26])
ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by Ar830

what does 4:26 mean?

ADD REPLYlink written 2.8 years ago by 12021560-00210

It is vector index in R. It means pick the elements from 4 to 26. I would highly recommend you to go thru some R programming basics before you start with microarray analysis.

ADD REPLYlink written 2.8 years ago by Ar830
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