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InSilico 和 virtualArray 这两个 Bioconductor 哪个更适合合并芯片....

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发表于 2017-6-8 11:11:21 | 显示全部楼层 |阅读模式
用过的同学来说一下吧:
insilicoDB, https://insilicodb.org/ may be useful as they allow a user to combine different published datasets for free.
The Bioconductor package virtualArray was designed to perform exactly what you are looking for.

其中InSilico还有非常多的合并统计学方法供选择:
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#combine them
>esets = list(eset1, eset2);
>eset = merge(esets, method="NONE");

The merge method allows you to apply various batch removal effect algorithms:

>eset = merge(esets, method="NONE");
>eset = merge(esets, method="COMBAT");
>eset = merge(esets, method="XPN");
>eset = merge(esets, method="DWD");
>eset = merge(esets, method="GENENORM"); 

 




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 楼主| 发表于 2017-6-8 11:12:06 | 显示全部楼层
You should carefully annotate/check annotation for both of your dataset before merging. Many to one, one to many and many to many these issues are quite common in annotation. Use InsilicoDB or virtual array whatever you like, but pay extra attention to your dataset annotation. Here's is an old article, which is basically for meta-analysis- but I am sure few of the steps would be common in your analysis as well.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2528050/

How can you combine different published expression datasets and analyze them in R?. Available from: https://www.researchgate.net/pos ... d_analyze_them_in_R [accessed Jun 8, 2017].
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