Question: Error in read.celfile.header(x) : Is GSE30521/CEL/GPL9793_gene_assignments.txt.gz really a CEL file
0
gravatar for muhammadzubair777
2.9 years ago by
muhammadzubair77710 wrote:

hello Dear! i am analyzing data through R and during analyzing , file read error is coming.

the using code is here. after readcell file there is an error give in box.

source("http://bioconductor.org/biocLite.R")

biocLite("huex10sttranscriptcluster.db")

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

library(GEOquery)

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)

Error in read.celfile.header(x) :

Is GSE30521/CEL/GPL9793_gene_assignments.txt.gz really a CEL file? tried reading as text, gzipped text, binary, gzipped binary, command console and gzipped command console formats

anyone help me to solve this problem.

ADD COMMENTlink written 2.9 years ago by muhammadzubair77710
0
gravatar for PoGibas
2.9 years ago by
PoGibas4.8k
Vilnius
PoGibas4.8k wrote:

You are reading in NOT a cell file, that's the problem (R tells you this Is GSE30521/CEL/GPL9793_gene_assignments.txt.gz really a CEL file).

Try using pattern option in list.files so you would get only cell files. As now you are listing all files in directory.

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

Also, this line is useless.

tarfile<- grep("\.tar$", rownames(gse30521raw), value = TRUE)
ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by PoGibas4.8k

ARE U SAYING LIKE THIS

list.files("GSE30521", pattern="*.CEL")

[1] "GSM756911.CEL.gz" "GSM756912.CEL.gz" "GSM756913.CEL.gz" "GSM756914.CEL.gz" "GSM756915.CEL.gz" "GSM756916.CEL.gz" "GSM756917.CEL.gz" "GSM756918.CEL.gz" [9] "GSM756919.CEL.gz" "GSM756920.CEL.gz" "GSM756921.CEL.gz" "GSM756922.CEL.gz" "GSM756923.CEL.gz" "GSM756924.CEL.gz" "GSM756925.CEL.gz" "GSM756926.CEL.gz" [17] "GSM756927.CEL.gz" "GSM756928.CEL.gz" "GSM756929.CEL.gz" "GSM756930.CEL.gz" "GSM756931.CEL.gz" "GSM756932.CEL.gz" "GSM756933.CEL.gz"

rawData<- read.celfiles(celfiles)

Error: These do not exist: GSM756911.CEL.gz GSM756912.CEL.gz GSM756913.CEL.gz GSM756914.CEL.gz GSM756915.CEL.gz GSM756916.CEL.gz GSM756917.CEL.gz GSM756918.CEL.gz GSM756919.CEL.gz GSM756920.CEL.gz GSM756921.CEL.gz GSM756922.CEL.gz GSM756923.CEL.gz GSM756924.CEL.gz GSM756925.CEL.gz GSM756926.CEL.gz GSM756927.CEL.gz GSM756928.CEL.gz GSM756929.CEL.gz GSM756930.CEL.gz GSM756931.CEL.gz GSM756932.CEL.gz GSM756933.CEL.gz

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by muhammadzubair77710

can you help me by modifying script?

ADD REPLYlink written 2.9 years ago by muhammadzubair77710

read.celfiles assumes that files are in the current working directory, while in you case they are in GSE30521/CEL, i.e, you need full path to your files.

ADD REPLYlink written 2.9 years ago by PoGibas4.8k
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