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Wednesday, March 4, 2009

Bioinfomatics in a spreadsheet?

This is an old article, but it just came to my attention today.

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

The title really does say it all. Alas, I just tested it with openoffice 3.0, and it has the same problem.

Good thing I do my gene name storage in databases!



Anonymous Anonymous said...

8 authors for such a paper? give me a break.

March 4, 2009 11:29:00 AM PST  
Blogger Anthony Fejes said...

One for each screen shot, one to find the error, one to write the macro to correct the problem and one to write the paper... oh wait, that's still just 7. What did the 8th person do?

March 4, 2009 11:46:00 AM PST  
Blogger Cath@VWXYNot? said...

"secured funds and provided intellectual leadership", probably.

March 6, 2009 3:32:00 PM PST  
Anonymous Anonymous said...

This is the third mention of Excel/OO converting names to dates that I have seen in the past 2 weeks. Funny.

An aside, if you have control over the data and a spreadsheet is the target, there are two possible options I have seen:
1) change the name to a formula with the gene name quoted (Sep-9 --> ="Sep-9")
2) Prefix an apostrophe (Sep-9 --> 'Sep-9)

March 8, 2009 12:22:00 PM PDT  
Blogger Anthony Fejes said...

I've also been told that you can set a field to "text" format while importing documents, which will then preserve the names. The only issue is if you're using a field that doesn't have an explicit type, which can be avoided fairly easily, if you know you need to avoid it.

March 9, 2009 1:52:00 PM PDT  

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