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GEO Microarray Data Cleaning

PostPosted: Tue Feb 20, 2018 2:41 pm
by stefmoore
To clean the GEO Dataset GSE84010, I did the following:

1) Go to https://www.ncbi.nlm.nih.gov/geo/ and search for the dataset GSE84010.
2) Download the Series Matrix File(s) (TXT Format).
3) Click on its corresponding platform GPL22111.
4) Click "View full table..." and copy & paste text into Notepad, saving it as a TXT file.
5) Open R Studio and use Efrain's code posted in GitLab to clean the dataset.
a. The most recently updated version of the code RCleanDscret.R as of 20Feb18 is attached.
b. Be sure to install the necessary libraries before running the code (pryr, MASS, dplyr, tidyr, readr, stringr).
c. Copy & paste the code into R Studio & run.
d. Select the downloaded Series Matrix File(s).
e. Select the relevant platform file.
f. Check for errors.
6) When the code is finished running, it should produce 3 files in your working directory which are attached.
a. GSE84010aftexcel - Clean dataset
b. GSE84010zscore - Normalized dataset
c. GSE84010dscrt - Discretized dataset

Re: GEO Microarray Data Cleaning

PostPosted: Tue Mar 13, 2018 1:52 pm
by stefmoore
**UPDATE**

The attached code RCleanDscret.R is an updated version of Efrain's code as of 13Mar18. Running this code in R Studio using the previous example dataset GSE84010 should now produce 4 files in your working directory: the three that were produced before, as well as one additional file GSE84010avg.txt, which is also attached. This file contains gene averages.

Re: GEO Microarray Data Cleaning

PostPosted: Mon Apr 02, 2018 10:45 pm
by DanielTira
Files for GSE83130

Re: GEO Microarray Data Cleaning

PostPosted: Mon Apr 02, 2018 11:27 pm
by DanielTira
Files for GSE77259

Re: GEO Microarray Data Cleaning

PostPosted: Mon Apr 02, 2018 11:35 pm
by DanielTira
Files for GSE7344

Re: GEO Microarray Data Cleaning

PostPosted: Thu Apr 05, 2018 11:59 am
by DanielTira
Files for GSE70678

Re: GEO Microarray Data Cleaning

PostPosted: Thu Apr 05, 2018 12:28 pm
by DanielTira
Files for GSE70460

Files removed GPL cleaning ERROR

Re: GEO Microarray Data Cleaning

PostPosted: Thu Apr 05, 2018 1:08 pm
by DanielTira
Files for GSE67850

Re: GEO Microarray Data Cleaning

PostPosted: Thu Apr 05, 2018 1:10 pm
by DanielTira
Part 1 of GSE63670

Files Removed GPL Cleaning ERROR

Re: GEO Microarray Data Cleaning

PostPosted: Thu Apr 05, 2018 1:11 pm
by DanielTira
Part 2 of GSE63670

Files Removed GPL Cleaning ERROR