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Archived Comments for: Mistaken Identifiers: Gene name errors can be introduced inadvertently when using Excel in bioinformatics

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  1. not only excel

    Heikki Lehvaslaiho, European Bioinformatics Institute

    30 June 2004

    I quickly tested a few common open source spreadsheet programs, calc, gnumeric and kspread, for this automatic symbol mutation ability.

    The following crude text table indicates if the conversions happens by default in these programs. "date" means that DEC1 type string gets converted, "float" means that RIKEN identifiers of type "2310009E13" get converted.



    Be careful out there!

    Competing interests

    None declared

  2. Well spotted

    Andrew Clegg, Birkbeck

    21 July 2004

    One to pin up on lab walls everywhere. I shudder to think how many pieces of work this might have affected.

    Competing interests

    None declared

  3. Special Interest group on spreadsheet risks

    Patrick OBeirne, Eusprig

    26 July 2004

    The European Spreadsheet Risk Interest Group (EUSPRIG) discusses the prevention and detection of spreadsheet errors. You can read about the emergence of the discipline of Spreadsheet Engineering and other related information at our website <a href=""></a>. We have just completed our fifth international conference and now have a corpus of approximately 100 peer reviewed papers in our subject domain.

    For more reports of spreadsheet errors, see

    <a href="">our stories</a>

    We're not specifically a group to discuss Excel bugs and workarounds, the <a href="">Excel-L list</a> is a very busy source of information on these, as well of course as the MS Knowledgebase.

    We are very interested in hearing from users about how you mitigate spreadsheet risks, what good practices they adopt, and so on. We are working with the ECDL Foundation for a syllabus of good practice for end users.

    Patrick O'Beirne, chair, Eusprig

    Competing interests


  4. Good point.

    Carol Bult, The Jackson Laboratory

    27 July 2004

    The article raises a very good point. I've experienced similar behavior in excel for other data types. I would add that it is always a good idea to carry along a unique numeric database id along with gene names/symbols. Database accession ids may be less likely to be munged by Excel (unless the ids are alpha-numeric!) and since they are usually unique and permanent they can be used to restore and/or update lists of gene names/symbols (which change all of the time).

    Competing interests

    No competing interests

  5. 19 probe sets in Affymetrix's human U133Plus2.0

    Chao Lu, Hospital for Sick Children, Toronto

    28 July 2004

    A good point. Many people did not pay attention to this 'small' error.

    Here is a list of 19 probe sets with errors in their gene symbol (June 23, 04 annotation, Affymetrix) when opened in Excel:

    1570394_at ===> 1-Sep

    200902_at ===> 15-Sep

    208999_at ===> 8-Sep

    209000_s_at ===> 8-Sep

    212413_at ===> 6-Sep

    212414_s_at ===> 6-Sep

    212415_at ===> 6-Sep

    212698_s_at ===> 10-Sep

    213666_at ===> 6-Sep

    214298_x_at ===> 6-Sep

    214720_x_at ===> 10-Sep

    220781_at ===> 1-Dec

    221129_at ===> 2-Apr

    223362_s_at ===> 3-Sep

    225814_at ===> 1-Sep

    226627_at ===> 8-Sep

    227034_at ===> 10-Sep

    227552_at ===> 1-Sep

    233632_s_at ===> 1-Sep

    Competing interests

    None declared

  6. And the lesson is...

    Neil Saunders, University of Queensland

    11 April 2008

    And that's why bioinformaticians don't use Excel for this purpose. Or more generally, don't use spreadsheets as "databases".

    Competing interests

    None declared

  7. MS should pick this up

    Richard Jackson, Independent

    12 May 2011

    I believe a large part of bioinformatics is about providing a conduit between experts in different fields, as well as novel discovery. Often, people have their own preferences for data manipulation packages, and frequently scientists with less technical expertise tend towards Excel. Moving data back and forth between individuals in such ways give ample opportunities for errors like this to arise.

    Hence, I think the situation is ubiquitous and serious enough to warrant intervention by Microsoft. I don't know if they've picked up on this article yet. Sadly, they don't seem to have anything in terms of a suggestion box on their website (I spent an hour looking!)

    Competing interests

    None declared