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如何合并多个study的芯片数据呢?

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发表于 2017-6-8 11:06:02 | 显示全部楼层 |阅读模式
我看到了这样一个问题,分享给大家
How can you combine different published expression datasets and analyze them in R?

I would like to perform a in-silico validation for my research study where I need to combine some published datasets (from GEO portal) to increase the number of samples (n) and then analyse them for differential expression for specific genes. I would to do all these analysis in R. Any suggestion for R software package, combining package or batch effect removal + their r scripts?
Thanks a lot for anticipation

最高票回答是;

InSilico DB has a "merging" R-Bioconductor package to combine public datasets from GEO. If you are not using R you can also combine data from the online platform (https://insilicodb.org)

Example:

[AppleScript] 纯文本查看 复制代码
# Retrieve 2 datasets
eset1 = getDataset(gse="GSE10072", gpl="GPL96", norm="ORIGINAL", genes=TRUE);
eset2 = getDataset(gse="GSE7670", gpl="GPL96", norm="ORIGINAL", genes=TRUE);

#combine them
esets = list(eset1, eset2);
eset = merge(esets, method="NONE");

#plot them
plotMDS(eset, targetAnnot="Disease", batchAnnot="Study");

InSilico DB packaged various batch removal effects methods so line 4 could be replaced with:

eset = merge(esets, method="XPN");
or
eset = merge(esets, method="COMBAT");


Hope this helps.

For more info Bioinformatics paper reference; InSilico DB and InSIlico Merging packages links, and blog link.

- Unlocking the potential of publicly available microarray data using inSilicoDb and inSilicoMerging R/Bioconductor packages -BMC Bioinfomatics [http://www.biomedcentral.com/1471-2105/13/335/abstract]

- inSilicoDb: an R/Bioconductor package for accessing human Affymetrix expert-curated datasets from GEO - Bioinformatics [http://bioinformatics.oxfordjournals.org/content/27/22/3204]

-Tutorial example : https://insilicodb.org/the-impac ... ifferent-data-sets/

R-Bioconductor packages:
http://www.bioconductor.org/pack ... tml/inSilicoDb.html
and
http://www.bioconductor.org/pack ... nSilicoMerging.html

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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 楼主| 发表于 2017-6-8 11:06:41 | 显示全部楼层
还有其它包推荐:
The Bioconductor package virtualArray was designed to perform exactly what you are looking for.

insilicoDB,
may be useful as they allow a user to combine different published datasets for free.

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发表于 2017-6-9 11:35:38 | 显示全部楼层
我测试了 inSilicoDb 这个包版本太低了,为了使用它我还得刻意安装低版本的R
[AppleScript] 纯文本查看 复制代码
package ‘inSilicoDb’ is not available (for R version 3.3.2) 
> library(inSilicoDb)
Error: package ‘inSilicoDb’ was built before R 3.0.0: please re-install it

你这个问题很复杂,需要打赏,请点击 http://www.bio-info-trainee.com/donate 进行打赏,谢谢
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发表于 2017-9-20 22:32:09 | 显示全部楼层
请问你们说的合并数据是合并的原始数据吗?还是已经处理过的excel 结果?一直没太明白。求指导
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