Page 4 of 4

Re: Master Table of GEO Brain Tumor Datasets

PostPosted: Mon Nov 30, 2020 9:00 am
by zgong001
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.

Re: Master Table of GEO Brain Tumor Datasets

PostPosted: Wed Dec 02, 2020 4:26 pm
by zgong001
The attachment is the updated dataset. Not standardized and discrete it.

Re: Master Table of GEO Brain Tumor Datasets

PostPosted: Wed Dec 02, 2020 9:27 pm
by rtanv003
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.

Re: Master Table of GEO Brain Tumor Datasets

PostPosted: Wed Dec 02, 2020 10:19 pm
by rtanv003
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.

Re: Master Table of GEO Brain Tumor Datasets

PostPosted: Thu Dec 17, 2020 9:01 am
by zgong001
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.

Descriptive statistics for the brain tumor datasets

PostPosted: Wed Feb 03, 2021 9:28 am
by zgong001
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.

Re: Master Table of GEO Brain Tumor Datasets

PostPosted: Fri Sep 17, 2021 7:07 pm
by khasan
Hello all,

Here I attached a file of some glioblastoma data. The file contains 10 data series posted after May 2018.

Re: Master Table of GEO Brain Tumor Datasets

PostPosted: Mon Oct 04, 2021 11:13 am
by khasan
Another Update of Glioblastoma Dataset

Re: Master Table of GEO Brain Tumor Datasets

PostPosted: Thu Oct 21, 2021 9:45 am
by khasan
Here is the publication list available in the TCGA website. 5 of them are related to brain tumor.