Abstract:
BACKGROUND:In this short article, we discuss a simple method for assessing sample size requirements in microarray experiments. RESULTS:Our method starts with the output from a permutation-based analysis for a set of pilot data, e.g. from the SAM package. Then for a given hypothesized mean difference and various samples sizes, we estimate the false discovery rate and false negative rate of a list of genes; these are also interpretable as per gene power and type I error. We also discuss application of our method to other kinds of response variables, for example survival outcomes. CONCLUSION:Our method seems to be useful for sample size assessment in microarray experiments.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Tibshirani Rdoi
10.1186/1471-2105-7-106keywords:
subject
Has Abstractpub_date
2006-03-02 00:00:00pages
106issn
1471-2105pii
1471-2105-7-106journal_volume
7pub_type
杂志文章abstract:BACKGROUND:DNA methylation of CpG dinucleotides is an essential epigenetic modification that plays a key role in transcription. Widely used DNA enrichment-based methods offer high coverage for measuring methylated CpG dinucleotides, with the lowest cost per CpG covered genome-wide. However, these methods measure the DN...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2574-7
更新日期:2018-12-22 00:00:00
abstract:BACKGROUND:Large-scale genomic studies often identify large gene lists, for example, the genes sharing the same expression patterns. The interpretation of these gene lists is generally achieved by extracting concepts overrepresented in the gene lists. This analysis often depends on manual annotation of genes based on c...
journal_title:BMC bioinformatics
pub_type: 杂志文章
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abstract:BACKGROUND:The advent of RNA interference techniques enables the selective silencing of biologically interesting genes in an efficient way. In combination with DNA microarray technology this enables researchers to gain insights into signaling pathways by observing downstream effects of individual knock-downs on gene ex...
journal_title:BMC bioinformatics
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abstract:BACKGROUND:Elevated sequencing error rates are the most predominant obstacle in single-nucleotide polymorphism (SNP) detection, which is a major goal in the bulk of current studies using next-generation sequencing (NGS). Beyond routinely handled generic sources of errors, certain base calling errors relate to specific ...
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pub_type: 杂志文章
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更新日期:2013-01-01 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2216-0
更新日期:2018-06-05 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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pub_type: 杂志文章
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journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0469-4
更新日期:2015-02-07 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2007-05-09 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-3164-z
更新日期:2019-11-08 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2014-11-04 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-359
更新日期:2008-09-01 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-392
更新日期:2010-07-22 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-371
更新日期:2007-10-03 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2010-05-25 00:00:00
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pub_type: 杂志文章
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更新日期:2012-10-03 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2015-11-04 00:00:00
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pub_type: 杂志文章
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journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-131
更新日期:2010-03-15 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-257
更新日期:2006-05-18 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0689-7
更新日期:2015-09-15 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-21
更新日期:2007-01-23 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2020-11-04 00:00:00
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journal_title:BMC bioinformatics
pub_type: 杂志文章
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更新日期:2008-04-21 00:00:00