New ways to butcher biological data using Excel

I must have a minor reputation as a critic of Excel in bioinformatics, since strangers are now sending contributions to my work email address. Thanks, you know who you are!

PLOS ONE  Online Survival Analysis Software to Assess the Prognostic Value of Biomarkers Using Transcriptomic Data in Non Small Cell Lung Cancer

When asked why I didn’t mask this email address, I replied “the authors didn’t”

This week: Online Survival Analysis Software to Assess the Prognostic Value of Biomarkers Using Transcriptomic Data in Non-Small-Cell Lung Cancer. Scroll on down to supporting Table S1 and right there on the page, staring you in the face is a rather unusual-looking microarray probeset ID.

I wonder if we should start collecting notable examples in one place?

To be fair, this is more human error than an issue with Excel per se, but I’m going to argue that using Excel promotes sloppy data management errors by making minds lazy :)

8 thoughts on “New ways to butcher biological data using Excel

  1. John

    This is terrible, but I can only be sympathetic to the person who made this mistake. I don’t know how often I have inadvertently typed something in a script or excel just because I forgot to mouse-focus on my web browser before trying to login to a website.

    1. nsaunders Post author

      Absolutely, we’ve all been there!

      I know that I tend to rant about these things; my aim isn’t blame or shame, but to raise awareness of the errors that can creep into publicly-available data when we are not vigilant.

  2. Jegar

    Good software shouldn’t allow you to make this sort of error. I feel for the creator of the document – poor thing having to work with Excel! So often these choices are driven by the other people (*cough cough* PI’s) in the research group who don’t want to learn more effective software like R, so you sigh and pull up Excel again. It is one of the burdens of the Statistician that we are often specialists in groups focusing on applied disciplines, so it is difficult to get across the importance of using the correct tools for the job.

    1. John

      The problem lies with some journals as well for not accepting plain text as supp mat. The submission system often will automatically convert it to PDF.

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