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Question: Cannot load CEL files
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gravatar for josejotero
28 days ago by
josejotero0
josejotero0 wrote:

I cannot open .CEL files without getting an error. I am using a new computer and can't find out why I have these settings. 

 

Here is the code:

data_eg <- ReadAffy("~/Downloads/GSE17204_RAW/GSM430339.CEL")
Error in read.celfile.header(as.character(filenames[[1]])) : 
  Could not open file ~/Downloads/GSE17204_RAW/GSM430339.CEL

 

Please help. I know that it is something stupid. I am running R v3.4.2.

 

ADD COMMENTlink modified 27 days ago by James W. MacDonald45k • written 28 days ago by josejotero0
1

does file.exists("~/Downloads/GSE17204_RAW/GSM430339.CEL") yield TRUE?

ADD REPLYlink written 28 days ago by Vincent J. Carey, Jr.6.2k

It yeilded FALSE. So I copy and pasted the file to another directory, and then it yields TRUE.

Then, I tried this:

data <- ReadAffy("~/Documents/Projects/Catherine Astrocyte project/Transcriptional data/162-2129.CEL")
Error in read.celfile.header(as.character(filenames[[1]])) : 
  Could not open file ~/Documents/Projects/Catherine Astrocyte project/Transcriptional data/162-2129.CEL

 

--and then on another file---

ta <- ReadAffy("~/Documents/Projects/Catherine Astrocyte project/Playing with the affy data/GSM430341.CEL")
Error in read.celfile.header(as.character(filenames[[1]])) : 
  Could not open file ~/Documents/Projects/Catherine Astrocyte project/Playing with the affy data/GSM430341.CEL

 

 

ADD REPLYlink written 28 days ago by josejotero0
1
gravatar for James W. MacDonald
27 days ago by
United States
James W. MacDonald45k wrote:

The error you are getting is, for like 99.999% of all such errors, an indication that the file isn't where you are pointing. So two things. First, there is usually no profit in running R in one directory and operating on files in another directory. I would recommend utilizing the principle that the working directory contains all of your code and the files upon which the code operates as a general rule. Having things here and there is a recipe for unintended errors.

Second, there is no need to be downloading things by hand. You can use the GEOquery package to get what you need.

> library(GEOquery)

> getGEOSuppFiles("GSE17204")
https://ftp.ncbi.nlm.nih.gov/geo/series/GSE17nnn/GSE17204/suppl/
OK
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE17nnn/GSE17204/suppl//GSE17204_RAW.tar'
Content type 'application/x-tar' length 18616320 bytes (17.8 MB)
downloaded 17.8 MB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE17nnn/GSE17204/suppl//filelist.txt'
Content type 'text/plain' length 524 bytes
downloaded 524 bytes

> setwd("GSE17204/")
> untar("GSE17204_RAW.tar")
> library(oligo)

> dat <- read.celfiles(dir(".", "CEL.gz"))
Loading required package: pd.hg.u133a.2
Loading required package: RSQLite
Loading required package: DBI
Platform design info loaded.
Reading in : GSM430339.CEL.gz
Reading in : GSM430340.CEL.gz
Reading in : GSM430341.CEL.gz
Reading in : GSM430342.CEL.gz
Reading in : GSM430343.CEL.gz
Reading in : GSM430344.CEL.gz
Reading in : GSM430345.CEL.gz
Reading in : GSM430346.CEL.gz
> eset <- rma(dat)
Background correcting
Normalizing
Calculating Expression
> eset
ExpressionSet (storageMode: lockedEnvironment)
assayData: 22277 features, 8 samples
  element names: exprs
protocolData
  rowNames: GSM430339.CEL.gz GSM430340.CEL.gz ... GSM430346.CEL.gz (8
    total)
  varLabels: exprs dates
  varMetadata: labelDescription channel
phenoData
  rowNames: GSM430339.CEL.gz GSM430340.CEL.gz ... GSM430346.CEL.gz (8
    total)
  varLabels: index
  varMetadata: labelDescription channel
featureData: none
experimentData: use 'experimentData(object)'
Annotation: pd.hg.u133a.2
>
ADD COMMENTlink written 27 days ago by James W. MacDonald45k

I took your advice, and I get the following:

> getwd()
[1] "/Users/oter04/Rcodes"
> dir()
[1] "162-2129.CEL" "2133.CEL"    
> ReadAffy("~/Rcodes/162-2129.CEL")
Error in read.celfile.header(as.character(filenames[[1]])) : 
  Could not open file ~/Rcodes/162-2129.CEL

Also, when I requestthe GEOquery, I get this: 


> library(GEOquery)
Error in library(GEOquery) : there is no package called ‘GEOquery’
> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.5 (BiocInstaller 1.26.1), ?biocLite for help
> biocLite(GEOquery)
Error in "BiocUpgrade" %in% pkgs : object 'GEOquery' not found

ADD REPLYlink written 27 days ago by josejotero0

I take my earlier statement back. The error you get is more likely due to lack of permissions.

> system("chmod 300 4105.CEL")
> system("ls -la 4105.CEL")
--wx------ 1 jmacdon adamusr-data5 14270951 Sep 22  2014 4105.CEL
> ReadAffy("4105.CEL")
Error in read.celfile.header(as.character(filenames[[1]])) :
  Could not open file 4105.CEL
> system("chmod 700 4105.CEL")
> ReadAffy("4105.CEL")
AffyBatch object
size of arrays=1190x1190 features (17 kb)
cdf=CynGene-1_0-st (??? affyids)
number of samples=1

So you probably need to change permissions on your files.

Also, from ?biocLite:

Arguments:

    pkgs: 'character()' of package names to install or update.  A
          missing value and 'suppressUpdates=FALSE' updates installed
          packages, perhaps also installing 'Biobase', 'IRanges', and
          'AnnotationDbi' if they are not already installed. Package
          names containing a '/' are treated as github repositories and
          installed using the 'install_github()' function of the
          'devtools' package.

You need to pass a character vector of packages you want to install to GEOquery, otherwise, the function thinks you are passing in an R object and tries to parse it.

ADD REPLYlink written 27 days ago by James W. MacDonald45k
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