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metaboanalyst一个处理蛋白或代谢数据的网站

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发表于 2017-6-10 11:08:05 | 显示全部楼层 |阅读模式

metaboanalyst是一个处理代谢的网站,
http://www.metaboanalyst.ca/face ... alizationView.xhtml选择的数据要.csv格式,可以用excel另存为.csv的格式。
根据自己的样本选择:
Samples in rows (unpaired)
Samples in columns(unpaired)
Samples in rows (paired)
Samples in columns(paired)
提交数据没有固定格式的,不过数据要处理成这样的形式:
AccessionN1N2N3P1P2P3
labelNNNPPP
E9Q363
0.256106
0.261089
0.292522
1.54457
1.533554
1.544754
A0A0R4J0W6
0.532173
0.556334
0.552752
1.347639
1.33907
1.322365
P62855
0.699128
0.703471
0.701404
1.161354
1.165385
1.182148
才能提交的。
如果当中有空值可以根据自己的数据处理:一般是用均值来替换,也可以用最小值来替换,当然有些就直接忽略。
也有选择看是不是要选择数据当中大于50%的值做为保留的。
下面是数据的标准化有四种方式:
Data scaling
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None
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Mean centering(mean-centered only)
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Auto scaling(mean-centered and divided by the standard deviation of each variable)
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Pareto scaling(mean-centered and divided by the square root of standard deviation of each variable)
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Range scaling(mean-centered and divided by the range of each variable)
是否对数据取Log值:
Data transformation
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None
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Log transformation(generalized logarithm transformation or glog)
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Cube root transformation(take cube root of data values)


下面是数据结果的展示:

Univariate Analysis
Fold Change AnalysisT-testsVolcano plot
One-way Analysis of Variance (ANOVA)
Correlation AnalysisPattern Searching
Chemometrics Analysis
Principal Component Analysis (PCA)
Partial Least Squares - Discriminant Analysis (PLS-DA)
Sparse Partial Least Squares - Discriminant Analysis (sPLS-DA)
Orthogonal Partial Least Squares - Discriminant Analysis (orthoPLS-DA)
Feature Identification
Significance Analysis of Microarray (and Metabolites) (SAM)
Empirical Bayesian Analysis of Microarray (and Metabolites) (EBAM)
Cluster Analysis
Hierarchical Clustering:DendrogramHeatmaps
Partitional Clustering:K-meansSelf Organizing Map (SOM)
Classification & Feature Selection
Random Forest
Support Vector Machine (SVM)


可以看到相应的数据图片。有热图、PCA、PLS-DA、OPLS-DA,图片很好看可以根据自己的需要设置,有2维和3维。对于初学者很适用。
如:下面数据分加是PCA、PLS-DA、OPLS-DA

还有热图和火山图:

下面是数据下载:
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Result DownloadPlease download the result tables and images below (the "Download.zip" contains all the files in your home directory).
The PDF analysis report may not be generated due to some inherent issues in R and LaTeX. You can try to re-generate PDF using an alternative approach using the button below.
Generate Analysis Report
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