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reading CELfiles for Human Exon 1.0 ST Array [CDF: HuEx-1_0-st-v2,coreR3,A20071112,EP]

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
cel rna-seq software-error r
• 5,261 views • link
updated by Ram Ram • written by 12021560-002 • 12021560-002

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

• 1 views • link
written by ATRX ATRX

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)

• 1 views • link
written by 12021560-002 • 12021560-002

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])
• 1 views • link
written by ATRX ATRX

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