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

[Jack Zhu]

Hi Ryan,

Thanks for your message and I will look into this.

Jack


----
Yuelin Jack Zhu

Biologist (Bioinformatics)
Genetics Branch/CCR/NCI/NIH
Tel: (301)496-4527
FAX: (301) 402-3241
E-mail: zhujack at mail.nih.gov

On Thu, Nov 17, 2016 at 5:20 PM, Ryan C. Thompson <rct at thompsonclan.org>
wrote:

> 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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