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Question: Problem with data not found using pathview package
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gravatar for nurhafizah.nazari
2.5 years ago by
Malaysia
nurhafizah.nazari0 wrote:

Hello,

I have a problem with my data GSE12391 for pathview package. After I input my data in R package, >data(gse12391.d), its say that data set gse12391 nit found. How can I overcome this problem? 

Thank you.

ADD COMMENTlink modified 2.5 years ago by James W. MacDonald45k • written 2.5 years ago by nurhafizah.nazari0
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gravatar for James W. MacDonald
2.5 years ago by
United States
James W. MacDonald45k wrote:

In the vignette, a data set that comes with the package is used for the analysis, simply so the author can show an example of how to do things, and to give end users some data they can use if they want to replicate the vignette.

However, this shouldn't be used as an example of how you would do things 'in real life' with other data. In other words, if you are using GSE12391, then ideally you would use GEOquery to get the data, then you would use something like limma to do the analysis, after which you would use pathview to look at pathways that may be perturbed, using the set of 'top genes' from one or more contrasts.

ADD COMMENTlink written 2.5 years ago by James W. MacDonald45k
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