[Bioc-devel] SRAdb::sraConvert returns results in arbitrary order

Ryan C. Thompson rct at thompsonclan.org
Thu Nov 17 23:20:53 CET 2016


I was recently bitten by an unexpected behavior in the sraConvert 
function from the SRAdb package. I wanted to fetch the other SRA IDs 
associated with the SRX numbers of 32 samples, and I used the sraConvert 
function to do so. However, I did not realized that sraConvert returns 
the results in arbitrary order rather than sorting them in the same 
order as the input, so I just used cbind to add these IDs to my existing 
sample table. This effectively shuffled my samples, and I did not notice 
until far downstream when I started making PCA plots and the clustering 
made no sense.

I leave it up to the developers of the SRAdb package to decide whether 
or not this is a bug, but I think it should at least be documented that 
the sort order of the output of sraConvert is arbitrary and will not 
necessarily match the input.


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