[BioC] GEOsubmission help request

[Manca Marco (PATH)]

Dear Alexandre,

good morning.

It is my first time trying to submit an expression dataset to GEO and, after reading around the web a bit, I have decided to try to approach the task using the tool you have developed for R/Bioconductor.

Unfortunately I get stuck somewhere and the message I receive is not enlightening me in any way, thus I hope you might help me.

I have all my .CEL files ("ADV1.CEL","ADV2.CEL","ADV3.CEL","ADV4.CEL","ADV5.CEL","ADV6.CEL","ADV7.CEL","ADV8.CEL","ADV9.CEL","ADV10.CEL","ADV11.CEL","ADV12.CEL","ADV13.CEL","ADV14.CEL","ADV15.CEL","ADV16.CEL","EAR1.CEL","EAR2.CEL","EAR3.CEL","EAR4.CEL","EAR5.CEL","EAR6.CEL","EAR7.CEL","EAR8.CEL","EAR9.CEL","EAR10.CEL","EAR11.CEL","EAR12.CEL","EAR13.CEL") in the working directory, and I have prepared the sampleInfo.txt and seriesInfo.txt according to the instruction that you offer in your synthetic guide and saved them in the same directory.

Nevertheless, when I give the command:

> microarray2soft(c("1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19","20","21","22","23","24","25","26","27","28","29"), "sampleInfo.txt", EarlyAdvancedATHERO,"seriesInfo.txt",softname = "AdvEar.soft", expressionmatrix = "expressionNormalized.txt")

the system is reacting like this:

Loading sampleinfo...

Error in microarray2soft(c("1", "2", "3", "4", "5", "6", "7", "8", "9",  : 
  Non-existing raw data files:


I have tried uploading the dataset into a affybatch object named like the seriesName, but it doesn't look like it would be making any difference.

Where is microarray2soft looking for the raw data? What am I doing wrong?

Thank you in advance for your attention and support.

Best regards, Marco


--
Marco Manca, MD
University of Maastricht
Faculty of Health, Medicine and Life Sciences (FHML)
Cardiovascular Research Institute (CARIM)

Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands)
Visiting address: Experimental Vascular Pathology group, Dept of Pathology - Room5.08,  Maastricht University Medical Center, P. Debyelaan 25, 6229  HX Maastricht

E-mail: m.manca at maastrichtuniversity.nl
Office telephone: +31(0)433874633
Personal mobile: +31(0)626441205
Twitter: @markomanka


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