Contents
How to extract expression data from GSE dataset?
You should get what you were looking for with: The GSE has a metadata section, just like the other classes. However, it doesn’t have a GEODataTable. Instead, it contains two lists, accessible using GPLList and GSMList, that are each lists of GPL and GSM objects. I tested the code I posted on R 3.3.2 and I get access to the Data Table just fine.
How to turn an object into an object in S4?
Classes and instances. In S3, you can turn any object into an object of a particular class just by setting the class attribute. S4 is much stricter: you must define the representation of the call using setClass, and the only way to create it is through the constructer function new.
How is callnextmethod used in S4 advanced R?
In S4, it’s the callNextMethod that (surprise!) is used to call the next method. It figures out which method to call by pretending the current method doesn’t exist, and looking for the next closest match. First we set up the classes: two types of vehicle (car and truck), and two types of inspect.
What’s the difference between S3 and S4 object system?
Compared to S3, the S4 object system is much stricter, and much closer to other OO systems. I recommend you familiarise yourself with the way that [ [S3]] works before reading this document – many of underlying ideas are the same, but the implementation is much stricter. There are two major differences from S3:
How to use geomirror to download expression dataset?
Due to the poor internet speed of mainland China, the researchers can hardly downlaod the GEO dataset by getGEO function from GEOquery package. So I write this GEOmirror package which only offer geoChina function, it’s very easy to use, for example : geoChina (‘GSE1009’)
How are curated datasets used in the Geo platform?
Curated DataSets form the basis of GEO’s advanced data display and analysis features, including tools to identify differences in gene expression levels and cluster heatmaps. GEO Profiles are derived from GEO DataSets. Not all original submitter-supplied records have been assembled into curated DataSets yet.
How are GEO profiles derived from geo datasets?
GEO Profiles are derived from GEO DataSets. Not all original submitter-supplied records have been assembled into curated DataSets yet. The GEO DataSets database can be searched using many different attributes including keywords, organism, DataSet type and authors.
Where do I find the accession numbers for the Geo dataset?
The colored blocks in the middle provide information on the experimental variable subsets within the DataSet. Click on the Sample accession numbers (GSMxxx) to select Samples individually, or click on colored blocks and then on blinking arrows to select entire groups of Samples.
What are the different types of geo datasets?
The GEO DataSets database stores original submitter-supplied records (Series, Samples and Platforms) as well as curated DataSets. See the Overview for information about these different records types and how they are are related to each other.
How can I limit the number of samples in a geo dataset?
Click on the Sample accession numbers (GSMxxx) to select Samples individually, or click on colored blocks and then on blinking arrows to select entire groups of Samples. You may limit Samples in groups by unchecking the boxes for any groups or Samples you do not wish to include.