Master Table of GEO Brain Tumor Datasets

GEO Brain Tumor Microarray and RNA-seq Data Cleaning

Re: Master Table of GEO Brain Tumor Datasets

Postby zgong001 » Mon Nov 30, 2020 9:00 am

rtanv003 wrote:
zgong001 wrote:The attachments are the updated tables.
Male - 1, Female - 0, there are 720 males and 504 females, others are unknow.
Normal - 0, Disease - 1, there are 1127 disease and 128 normal


This caused some of the genes to convert into dates because this updating has been done by excel. This also resulted in two genes to have same names, which are MARC1(1-Mar) and MARCH1(1-Mar).



The dataset has no relationship with Excel. Even though you can use it to open the dataset, you don't need to open it with Excel. You should directly read the .csv file with Python.
zgong001
 
Posts: 413
Joined: Thu Nov 16, 2017 10:10 am

Re: Master Table of GEO Brain Tumor Datasets

Postby zgong001 » Wed Dec 02, 2020 4:26 pm

The attachment is the updated dataset. Not standardized and discrete it.
Attachments
MergerdGenes-1202.csv
(170.32 MiB) Downloaded 59 times
zgong001
 
Posts: 413
Joined: Thu Nov 16, 2017 10:10 am

Re: Master Table of GEO Brain Tumor Datasets

Postby rtanv003 » Wed Dec 02, 2020 9:27 pm

zgong001 wrote:The attachments are the updated tables.
Male - 1, Female - 0, there are 720 males and 504 females, others are unknow.
Normal - 0, Disease - 1, there are 1127 disease and 128 normal


I did some further cleaning. Now only glioblastoma patients are here with disease variable set to 1. This reduced the patients from 1201 to 414. And the samples with _x and _y, they both contained the same values and so one of them were kept without the subscript and other one was removed. Now there are 310 disease and 104 normal samples and 254 male samples and 160 female samples.
Attachments
Merged-discrete-cleaned-gbm-only.csv
(27.77 MiB) Downloaded 59 times
Merged-continue-cleaned-gbm-only.csv
(137.21 MiB) Downloaded 49 times
Last edited by rtanv003 on Wed Dec 02, 2020 10:37 pm, edited 1 time in total.
rtanv003
 
Posts: 4
Joined: Wed Aug 26, 2020 9:45 pm

Re: Master Table of GEO Brain Tumor Datasets

Postby rtanv003 » Wed Dec 02, 2020 10:19 pm

zgong001 wrote:The attachment is the updated dataset. Not standardized and discrete it.


The number of samples from this dataset and the continuous and discrete data that is uploaded uploaded before, they do not match up. There are some samples that are present in this one but not in the previous two and there are some that are present in the previous two datasets but not in this new one.

364 samples that are new in this recently uploaded dataset that are not present in the previous two. 704 samples that are in the old dataset (z-score continous and discretized) that are not in this new one.

These samples, coming from GSE62802, are missing in the new datasets and they are related to glioblastoma. please add them if you can-

GSM1533552
GSM1533553
GSM1533554
GSM1533555
GSM1533556
GSM1533557
GSM1533558
GSM1533559
GSM1533560
GSM1533561
GSM1533562
GSM1533563
GSM1533564

Please fix the sample inconsistency at your earliest convenience.
Thank you.
rtanv003
 
Posts: 4
Joined: Wed Aug 26, 2020 9:45 pm

Re: Master Table of GEO Brain Tumor Datasets

Postby zgong001 » Thu Dec 17, 2020 9:01 am

rtanv003 wrote:
zgong001 wrote:The attachment is the updated dataset. Not standardized and discrete it.


The number of samples from this dataset and the continuous and discrete data that is uploaded uploaded before, they do not match up. There are some samples that are present in this one but not in the previous two and there are some that are present in the previous two datasets but not in this new one.

364 samples that are new in this recently uploaded dataset that are not present in the previous two. 704 samples that are in the old dataset (z-score continous and discretized) that are not in this new one.

These samples, coming from GSE62802, are missing in the new datasets and they are related to glioblastoma. please add them if you can-

GSM1533552
GSM1533553
GSM1533554
GSM1533555
GSM1533556
GSM1533557
GSM1533558
GSM1533559
GSM1533560
GSM1533561
GSM1533562
GSM1533563
GSM1533564

Please fix the sample inconsistency at your earliest convenience.
Thank you.



Yes, GSE62802 should be include. I missed it.
zgong001
 
Posts: 413
Joined: Thu Nov 16, 2017 10:10 am

Descriptive statistics for the brain tumor datasets

Postby zgong001 » Wed Feb 03, 2021 9:28 am

The attachment is the Descriptive statistics for the brain tumor datasets. The value is log4 transform of mean of disease cases / mean of control cases.
Attachments
BrainTumor.docx
(93.47 KiB) Downloaded 55 times
zgong001
 
Posts: 413
Joined: Thu Nov 16, 2017 10:10 am

Re: Master Table of GEO Brain Tumor Datasets

Postby khasan » Fri Sep 17, 2021 7:07 pm

Hello all,

Here I attached a file of some glioblastoma data. The file contains 10 data series posted after May 2018.
Attachments
New_glioblastoma.xlsx
(17.38 KiB) Downloaded 30 times
khasan
 
Posts: 17
Joined: Mon May 17, 2021 2:13 pm

Re: Master Table of GEO Brain Tumor Datasets

Postby khasan » Mon Oct 04, 2021 11:13 am

Another Update of Glioblastoma Dataset
Attachments
New glioblastoma.xlsx
(22.46 KiB) Downloaded 35 times
khasan
 
Posts: 17
Joined: Mon May 17, 2021 2:13 pm

Re: Master Table of GEO Brain Tumor Datasets

Postby khasan » Thu Oct 21, 2021 9:45 am

Here is the publication list available in the TCGA website. 5 of them are related to brain tumor.
Attachments
TCGA Publication.docx
(16.4 KiB) Downloaded 25 times
khasan
 
Posts: 17
Joined: Mon May 17, 2021 2:13 pm

Previous

Return to Dataset Cleaning

Who is online

Users browsing this forum: No registered users and 1 guest

cron