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. 2004 Jun 23:5:80.
doi: 10.1186/1471-2105-5-80.

Mistaken identifiers: gene name errors can be introduced inadvertently when using Excel in bioinformatics

Barry R Zeeberg  1 , Joseph Riss, David W Kane, Kimberly J Bussey, Edward Uchio, W Marston Linehan, J Carl Barrett, John N Weinstein
Affiliations

Mistaken identifiers: gene name errors can be introduced inadvertently when using Excel in bioinformatics

Barry R Zeeberg et al. BMC Bioinformatics. .

Abstract

Background: When processing microarray data sets, we recently noticed that some gene names were being changed inadvertently to non-gene names.

Results: A little detective work traced the problem to default date format conversions and floating-point format conversions in the very useful Excel program package. The date conversions affect at least 30 gene names; the floating-point conversions affect at least 2,000 if Riken identifiers are included. These conversions are irreversible; the original gene names cannot be recovered.

Conclusions: Users of Excel for analyses involving gene names should be aware of this problem, which can cause genes, including medically important ones, to be lost from view and which has contaminated even carefully curated public databases. We provide work-arounds and scripts for circumventing the problem.

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Figures

Figure 1
Figure 1
Screen shot of Microsoft Excel spreadsheet illustrating errors caused by default conversion of gene names to dates. Columns A, E, and I contain the correct gene names. Columns B, F, and J contain the corresponding underlying internal Excel date representation resulting from the forced default date conversion. Columns C, G, and K contain the corresponding default format date conversions. To create this table, we prepared a tab-delimited text file in which each gene name was repeated three times side by side. The correct gene names in columns A, E, and I were retained by opening this text file with Excel, and selecting "text" mode for columns A, E, and I in the Text Import Wizard Step 3 of 3 that appears while opening a file in Excel. Subsequently, the format menu "number" option (with zero decimal places) was applied to columns B, F, and J to display the internal date format.
Figure 2
Figure 2
Screen shot of LocusLink from November 12, 2002 illustrating an error caused by default conversion of a gene name to date that had propagated from the human-mouse homology map data (Figure 3).
Figure 3
Figure 3
Screen shot of the human-mouse homology map from November 14, 2003 illustrating an error caused by default conversion of a gene name to date.
Figure 4
Figure 4
Script to scan for SymbolMutation error.
See this image and copyright information in PMC

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