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This article will explain in detail how GEOquery reads the local expression matrix compression package. The editor thinks it is very practical, so I share it for you as a reference. I hope you can get something after reading this article.

The getGEO () of the GEOquery package can be used to download chip-related data. However, some people reflect that many chip expression matrix downloads often make mistakes, and the matrix files can be downloaded to the corresponding work path by manual download:

The basic naming format of matrix files: GSEXXXXX_series_matrix.txt.gz

To avoid manual collation, you can use getGEO to read local matrix files, such as (take GSE66597 as an example):

Workdir = "F:/GEO/20180605/download/GSE66597" # set the work path setwd (workdir) gset = getGEO (filename= ". / GSE66597_series_matrix.txt.gz", AnnotGPL=TRUE,destdir=workdir)

In addition to reading the corresponding matrix file, you can also download its related platform annotation information file to the corresponding working directory (the save directory is set to the working directory).

After completing the reading of this city, the data can be extracted and sorted out according to the conventional method.

On "GEOquery how to read the local expression matrix compression package" this article is shared here, I hope the above content can be of some help to you, so that you can learn more knowledge, if you think the article is good, please share it out for more people to see.

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