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

by: BR Zeeberg, J Riss, DW Kane, KJ Bussey, E Uchio, WM Linehan, JC Barrett, JN Weinstein

BMC Bioinformatics, Vol. 5 (23 June 2004)

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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.

@article{citeulike:339459, 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.}, address = {Genomics \& Bioinformatics Group, Laboratory of Molecular Pharmacology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892 USA. barry@discover.nci.nih.gov}, author = {Zeeberg, B. R. and Riss, J. and Kane, D. W. and Bussey, K. J. and Uchio, E. and Linehan, W. M. and Barrett, J. C. and Weinstein, J. N. }, citeulike-article-id = {339459}, doi = {http://dx.doi.org/10.1186/1471-2105-5-80}, issn = {1471-2105}, journal = {BMC Bioinformatics}, keywords = {excel, gene}, month = {June}, posted-at = {2005-10-03 17:38:16}, priority = {0}, title = {Mistaken identifiers: gene name errors can be introduced inadvertently when using Excel in bioinformatics.}, url = {http://dx.doi.org/10.1186/1471-2105-5-80}, volume = {5}, year = {2004} }

RIS record

TY - JOUR ID - citeulike:339459 L3 - citeulike-article-id:339459 TI - Mistaken identifiers: gene name errors can be introduced inadvertently when using Excel in bioinformatics. JF - BMC Bioinformatics VL - 5 AD - Genomics & Bioinformatics Group, Laboratory of Molecular Pharmacology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892 USA. barry@discover.nci.nih.gov SN - 1471-2105 N2 - 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. KW - excel KW - gene AU - Zeeberg, BR AU - Riss, J AU - Kane, DW AU - Bussey, KJ AU - Uchio, E AU - Linehan, WM AU - Barrett, JC AU - Weinstein, JN PY - 2004/06/23/ UR - http://dx.doi.org/10.1186/1471-2105-5-80 ER -

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