Ask for help on the preprocessing of GEO microarray data with Oligo and affy package
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chziy429 • 0
@chziy429-22357
Last seen 23 months ago

I have downloaded the raw CEL data included in "GSE41418" from GEO and tried to process the raw microarray data according to the following Rscripts

affydata <- ReadAffy(cdfname = "mouse4302mmentrezgcdf") eset <- frma(affydata) or eset <- rma(affydata)

OR affydata<-read.celfiles(list.celfiles()) eset <- oligo::rma(affydata)

The raw data can be read by ReadAffy but failed in the normalization process. I have tried to process it with affy::rma, frma::frma and oligo::rma, but it still can not work. An error saying "address 0x7f854500a000, cause 'invalid permissions'" was returned. However this error message was not appeared in some other datasets like "GSE41342". I was wondering whether this file was corrupted. Could you please help me address this problem? Any suggestion and recommendation are welcome.

affy rma frma oligo • 344 views
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Please show your complete code, error and sessionInfo (as per forum guidelines), otherwise it is difficult/impossible to provide help.

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@james-w-macdonald-5106
Last seen 5 hours ago
United States
> library(GEOquery)
> getGEOSuppFiles("GSE41418")
<snip>
> setwd("GSE41418/")
> untar("GSE41418_RAW.tar")
> cels <- dir(".", "CEL.gz$")
> library(affy)
Bioconductor version 3.10 (BiocManager 1.30.7), ?BiocManager::install for help
> install.packages("http://mbni.org/customcdf/24.0.0/ensg.download/mouse4302mmensgcdf_24.0.0.tar.gz", repos = NULL, type = "source")
Installing package into 'C:/Users/jmacdon/AppData/Roaming/R/win-library/3.6'
(as 'lib' is unspecified)
trying URL 'http://mbni.org/customcdf/24.0.0/ensg.download/mouse4302mmensgcdf_24.0.0.tar.gz'
Content type 'application/octet-stream' length 2211467 bytes (2.1 MB)
downloaded 2.1 MB

* installing *source* package 'mouse4302mmensgcdf' ...
** using staged installation
<snip>
* DONE (mouse4302mmensgcdf)
> dat <- ReadAffy(filenames = cels, cdfname = "mouse4302mmensgcdf")
> eset <- rma(dat)
Background correcting
Normalizing
Calculating Expression
> eset
ExpressionSet (storageMode: lockedEnvironment)
assayData: 18198 features, 12 samples 
  element names: exprs 
protocolData
  sampleNames: GSM1016804_Harlan_cerulein_1.CEL.gz
    GSM1016805_Harlan_cerulein_2.CEL.gz ...
    GSM1016815_Jackson_Control_39.CEL.gz (12 total)
  varLabels: ScanDate
  varMetadata: labelDescription
phenoData
  sampleNames: GSM1016804_Harlan_cerulein_1.CEL.gz
    GSM1016805_Harlan_cerulein_2.CEL.gz ...
    GSM1016815_Jackson_Control_39.CEL.gz (12 total)
  varLabels: sample
  varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation: mouse4302mmensgcdf 

Maybe try re-downloading?

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