Geo2r: difference analysis of data in geo database

Welcome to your attention ” Shengxin cultivation manual ”!

GEO The data in the database is public , Many researchers will download the data and analyze it by themselves , Differential expression analysis is one of the most common analysis strategies , In order to facilitate better excavation GEO Data in , The official website provides a tool ​​GEO2R​​, It is convenient to analyze differences .

You can see from the name , The function of this tool is to GEO The data in the database is imported into R In language , And then we do a difference analysis , Essentially through the following two bioconductor Upper R Package implementation

1. GEOquery
2. limma
   

​​GEOquery​​​ For automatic download GEO data , And read R Environment ;​​limma​​ Is a classic difference analysis software , Used to perform variance analysis .

A set of samples in GEO In the database ​​series​​​ Express , such as ​​GSE25724​​, Contains case and control Two groups of samples ,case Group contains 6 A biological repetition ,control Group contains 7 A biological repetition , common 13 Samples , Links are as follows

​ ​https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25724​​

You can see... On the web page ​​GEO2R​​​ The button , Click this button to analyze , In addition to variance analysis ,​​GEO2R​​ It also provides some simple data visualization functions .

1.  Value distribution

This option displays the distribution of expression quantity in all samples with a box diagram , The results are as follows

2. Profile graph

This option is used to show a probe / Distribution of genes in all samples , The results are as follows

Click on ​​Sample values​​, You can see the corresponding expression value , It is shown as follows

​​GEO2R​​ The steps for variance analysis are as follows

1. Define sample groups

adopt ​​Define groups​​ Button to define sample groups , First enter a group Name , Then select the corresponding sample , It is shown as follows

2. Parameter adjustment

Through the ​​Options​​ menu , You can adjust the parameters for variance analysis , It is shown as follows

The first parameter is used to select the multiple hypothesis test P Value correction algorithm , The second parameter indicates whether to change the original expression quantity log transformation , The third parameter adjusts the corresponding... Shown in the final result platfrom Note information for , It is based on what the customer provides supplement  file Information in , Or use ​​soft​​ Information in the file .

3. perform

Click... As shown below ​​Top 250​​ Button , Perform variance analysis .

The results are as follows , Show only the most prominent... On the page 250 A differential gene

The results of all genes can be obtained by ​​Save all results​​​ export , adopt ​​GEO2R​​, It can be done without any programming foundation , Complete variance analysis in sequence .

·end·

— If you like , Share it with your friends —

Scan for microsignals , More exciting content is waiting for you ！