Question

SCAN.UPC giving error for multiple input files

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Vani ▴ 20

@vani-8145

Last seen 8.9 years ago

United States

Hi,

I am trying to use SCAN.UPC to normalize a dataset. Whenever I run the command

normalized = SCAN("GSE46224")

I get the error:

Error in downloadFromGEO(celFilePattern, expectedFileSuffixPattern = "*.CEL.gz") : 
  No raw data files could be downloaded from GEO for GSE46224

I checked on the geo site and cel files do exist for this dataset. I encountered this same issue with the GSE53080 dataset as well.

Please advise.

scan.upc • 1.7k views

ADD COMMENT • link updated 9.3 years ago by Stephen Piccolo ▴ 600 • written 9.3 years ago by Vani ▴ 20

score 0 · Answer 1 · 2015-08-11

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Stephen Piccolo ▴ 600

@stephen-piccolo-6761

Last seen 4.2 years ago

United States

Vani,

SCAN is designed to process gene expression data from Affymetrix microarrays and Agilent two-color microarrays. (I am working on a version that can process Agilent one-color microarrays and Illumina Beadchip arrays.) The data sets you mentioned in your question are RNA-Sequencing data sets, so SCAN is not designed to process them. However, you could apply the UPC method to them if you are interested. Please read the vignette if you haven't already, and let me know if you have questions.

-Steve

ADD COMMENT • link 9.3 years ago Stephen Piccolo ▴ 600

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Hi Mr.Piccolo,

So even if I downloaded the RNA-Seq CEL files and attempted to apply SCAN method, it would not work correct? Also I tried to use the UPC() :

normalized <- UPC("GSE46224")

And I still got the same error:

Error in downloadFromGEO(celFilePattern, expectedFileSuffixPattern = "*.CEL.gz") : 
  No raw data files could be downloaded from GEO for GSE46224

ADD REPLY • link 9.3 years ago Vani ▴ 20

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There is no such thing as a CEL file for RNA-Seq. Those are specific to Affymetrix microarrays. Have you read the vignette?

ADD REPLY • link 9.3 years ago Stephen Piccolo ▴ 600