Effects of sample size on differential gene expression, rank order and prediction accuracy of a gene signature.
Effects of sample size on differential gene expression, rank order and prediction accuracy of a gene signature.
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DOI：
10.1371/journal.pone.0065380
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Baracos VE
中科院分区：
文献类型：
--
作者：
Stretch C;Khan S;Asgarian N;Eisner R;Vaisipour S;Damaraju S;Graham K;Bathe OF;Steed H;Greiner R;Baracos VE
在不同研究之间，顶级差异表达基因列表往往不一致，有人认为，小样本容量导致判别模型中缺乏重复性和较差的预测精度。采用基因芯片技术对13 4例人骨骼肌活检标本进行性别差异分析(69♂，65♀)。使用完整的数据集和子样本(n = 10(5♂，5♀)到n = 120(60♂，60♀))来评估样本大小对单基因差异表达、基因排序和预测精度的影响。使用我们的完整数据集(n = 134)，我们识别了717个差异表达的转录本(p<；0.0001)，我们能够以∼90%的准确率预测性别，无论是在我们的数据集内还是在外部数据集上。使用较小的子样本，最高差异表达基因的p值和排序都变得更加可变。例如，在n = 10(5♂，5♀)处，在p<；0.0001处没有基因被认为是差异表达，并且预测准确率为∼50%(不比Chance好)。我们发现，样本量明显影响微阵列分析结果；样本量小会导致基因列表不稳定，预测精度较差。我们预计，这将适用于其他表型，除了性别。
Top differentially expressed gene lists are often inconsistent between studies and it has been suggested that small sample sizes contribute to lack of reproducibility and poor prediction accuracy in discriminative models. We considered sex differences (69♂, 65♀) in 134 human skeletal muscle biopsies using DNA microarray. The full dataset and subsamples (n = 10 (5♂, 5♀) to n = 120 (60♂, 60♀)) thereof were used to assess the effect of sample size on the differential expression of single genes, gene rank order and prediction accuracy. Using our full dataset (n = 134), we identified 717 differentially expressed transcripts (p<0.0001) and we were able predict sex with ∼90% accuracy, both within our dataset and on external datasets. Both p-values and rank order of top differentially expressed genes became more variable using smaller subsamples. For example, at n = 10 (5♂, 5♀), no gene was considered differentially expressed at p<0.0001 and prediction accuracy was ∼50% (no better than chance). We found that sample size clearly affects microarray analysis results; small sample sizes result in unstable gene lists and poor prediction accuracy. We anticipate this will apply to other phenotypes, in addition to sex.
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影响因子：
8.8
作者：
Simon, R
通讯作者：
Simon, R
影响因子：
3.3
作者：
Shen, W;Punyanitya, M;Heshka, S
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Heshka, S
影响因子：
168.9
作者：
Michiels, S;Koscielny, S;Hill, C
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Hill, C
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y
影响因子：
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作者：
Maher AC;Fu MH;Isfort RJ;Varbanov AR;Qu XA;Tarnopolsky MA
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Tarnopolsky MA