I'm trying to submit to sub-challenge 2, however, I can't seem to open the data files when I submit to the express lane challenge.
From the wiki (https://www.synapse.org/#!Synapse:syn6187098/wiki/449443), I expected the test data files to be in either '/test-data/' or './test-data/', and tried both.
However, I get an error message like this in the log file:
Error in file(file, "rt") : cannot open the connection
Calls: read.csv -> read.table -> file
In addition: Warning message:
In file(file, "rt") :
cannot open file '/test-data/dfci.2009_entrezID_TPM_hg19.csv': No such file or directory
Execution halted
Does anyone know where the test data is actually located? Or are the file names different than what's reported in the wiki? Or do I have to do something else to make the test data appear?
Thank you,
-S
Created by Sam Danziger sdanziger Dear Sam,
Please do not use hard coded paths in your script, except for the sc2 clinical file. When you read in the sc2 clinical file which is at `/test-data/sc2_Validation_ClinAnnotations.csv`, the location of the dfci file can be found under this column: RNASeq_geneLevelExpFile of that file. That being said, the filename that we put on the wiki is incorrect. The file is actually named:
`/test-data/dfci.2009_entrezID_TPM_hg19_LBR1.csv` Apologies for the inconvenience.
Best,
Tom
Drop files to upload
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