Question: SCAN.UPC giving error for multiple input files
0
gravatar for Vani
4.2 years ago by
Vani20
United States
Vani20 wrote:

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 • 744 views
ADD COMMENTlink modified 4.2 years ago by Stephen Piccolo560 • written 4.2 years ago by Vani20
Answer: SCAN.UPC giving error for multiple input files
0
gravatar for Stephen Piccolo
4.2 years ago by
United States
Stephen Piccolo560 wrote:

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 COMMENTlink written 4.2 years ago by Stephen Piccolo560

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 REPLYlink modified 4.2 years ago • written 4.2 years ago by Vani20

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

ADD REPLYlink written 4.2 years ago by Stephen Piccolo560
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