Hello,
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.
-Ryan
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