Error of GDS2eSet() function
1
0
Entering edit mode
vahideh • 0
@vahideh-9470
Last seen 4.3 years ago

Hi,

I try to convert GDS file with following code:

gds<- getGEO(filename = system.file("extdata/GDS2364_full.soft.gz", package = "GEOquery"))
eset = GDS2eSet(gds,do.log2=TRUE,GPL=NULL,AnnotGPL=TRUE,getGPL=TRUE)

But this error is displayed:

Using locally cached version of GPL534 found here:
C:\Users\RAYANE~1\AppData\Local\Temp\RtmpUzoG8i/GPL534.annot.gz Using locally cached version of GPL534 found here:
C:\Users\RAYANE~1\AppData\Local\Temp\RtmpUzoG8i/GPL534.annot.gz 
Error in gzfile(fname, open = "rt") : invalid 'description' argument
In addition: Warning messages:
1: In GDS2eSet(gds, do.log2 = TRUE, GPL = NULL, AnnotGPL = TRUE, getGPL = TRUE) :
  NaNs produced
2: In if (GSEMatrix & geotype == "GSE") { :
  the condition has length > 1 and only the first element will be used
3: In if (geotype == "GDS") { :
  the condition has length > 1 and only the first element will be used
4: In if (geotype == "GSE" & amount == "full") { :
  the condition has length > 1 and only the first element will be used
5: In if (geotype == "GSE" & amount != "full" & amount != "table") { :
  the condition has length > 1 and only the first element will be used
6: In if (geotype == "GPL") { :
  the condition has length > 1 and only the first element will be used
7: In if (!file.exists(destfile)) { :
  the condition has length > 1 and only the first element will be used

Please help me to resolve my problem!

Thank you!

convert geoquery error GDS2eSet • 1.0k views
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1
Entering edit mode
@james-w-macdonald-5106
Last seen 9 hours ago
United States

There appear to be two problems here. First, it looks like you downloaded the data by hand, and put the file in your package library. You should never do something like that! Messing around with the package library directory is a really good way to completely bork your R installation.

Instead, you should just use getGEO() to download things. It will put the files in a temporary directory, which is as it should be. I'm not sure why one would want a GDS over a GSE, but when I get GEO data, I always get the GSE because it directly results in the creation of an ExpressionSet:

> eset <- getGEO("GSE4735", AnnotGPL = TRUE)[[1]]
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE4nnn/GSE4735/matrix/
Found 1 file(s)
GSE4735_series_matrix.txt.gz
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE4nnn/GSE4735/matrix/GSE4735_series_matrix.txt.gz'
downloaded 111 KB

File stored at:
C:\Users\jmacdon\AppData\Local\Temp\Rtmp0qEraW/GPL534.annot.gz
There were 30 warnings (use warnings() to see them)
> eset
ExpressionSet (storageMode: lockedEnvironment)
assayData: 4608 features, 4 samples
  element names: exprs
protocolData: none
phenoData
  sampleNames: GSM106991 GSM107053 GSM107054 GSM107055
  varLabels: title geo_accession ... data_row_count (39 total)
  varMetadata: labelDescription
featureData
  featureNames: 1.1.1.1 1.1.1.10 ... 4.4.9.9 (4608 total)
  fvarLabels: ID Gene title ... GO:Component ID (21 total)
  fvarMetadata: Column Description labelDescription
experimentData: use 'experimentData(object)'
Annotation: GPL534

 

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