Master Table of GEO Brain Tumor Datasets

GEO Brain Tumor Microarray and RNA-seq Data Cleaning

Master Table of GEO Brain Tumor Datasets

Postby cwyoo » Fri Feb 02, 2018 9:31 am

Master Table of GEO Brain Tumor Datasets
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Re: Master Table of GEO Brain Tumor Datasets

Postby stefmoore » Mon Feb 05, 2018 12:37 pm

Hello all,

Please find attached the list of brain tumor datasets compiled by Lauren. I do not know when her last search was performed. We are working specifically with those datasets on the microarray tabs.
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Brain Tumor Datasets 5Feb18.xlsx
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Re: Master Table of GEO Brain Tumor Datasets

Postby DanielTira » Thu Sep 20, 2018 11:30 am

Latest master list that includes completed summer GSEs. Could use a little more organization that I'll do with a bigger screen and replace this one.
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Brain Tumor Datasets 20 September 2018.ods
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Re: Master Table of GEO Brain Tumor Datasets

Postby zgong001 » Thu Sep 27, 2018 2:17 pm

I checked the Master Table of GEO Brain Datasets and marked it with different color. Red means that some data is missing. Purple means some gene name was not changed. Green means the data is good and no problem. Yellow means there was some error during cleaning and cleaning was not finished. White means the dataset was not cleaned.
Attachments
Brain Tumor Datasets 20 September 2018 (checked).xlsx
Checked Brain Tumor
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Re: Master Table of GEO Brain Tumor Datasets

Postby zgong001 » Thu Oct 25, 2018 2:42 pm

The attachment is the most updated master table of GEO Brain Tumor datasets. The yellow parts of it are the datasets which can't be cleaned up because of no data or no gene name.
Attachments
Brain Tumor Datasets 20 September 2018 (checked -10-23-2018).xlsx
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Master Table of GEO Brain Tumor Datasets (updated)

Postby zgong001 » Mon Dec 17, 2018 9:35 am

The attachments are updated Master Table of GEO Brain Tumor Datasets.
In Column 3 and Column 4, number of gene and number of sample were listed.
Attachments
Brain Tumor Datasets 20 September 2018 (checked -12-13-2018).xlsx
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Merged dataset of Glioblastoma

Postby zgong001 » Fri Feb 22, 2019 11:17 am

I merged some datasets of Glioblastoma, then finally got 5754 genes and 619 subjects. The merged datasets are

GSE31545
GSE63035
GSE34824
GSE24558
GSE10878
GSE25632
GSE42670
GSE81934
GSE36245
GSE9885
GSE10878
GSE7344
GSE49822
GSE53228
GSE6014
GSE36426
GSE32374
Attachments
Merged-Gliobastoma.csv
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Re: Merged dataset of Glioblastoma

Postby cwyoo » Thu Feb 28, 2019 7:08 am

zgong001 wrote:I merged some datasets of Glioblastoma, then finally got 5754 genes and 619 subjects. The merged datasets are

GSE31545
GSE63035
GSE34824
GSE24558
GSE10878
GSE25632
GSE42670
GSE81934
GSE36245
GSE9885
GSE10878
GSE7344
GSE49822
GSE53228
GSE6014
GSE36426
GSE32374


In the merged Glioblastoma (and Astrocytoma) dataset,
* you should have a clinical variable representing Glioblastoma stages (where 0 represent normal subjects). I do not see it. In Astrocytoma dataset, Astrocytoma stages should be in the merged dataset as well.
* no missing data (I see missing data in some variables, e.g., age, sex). the GEO studies that have missing clinical variables, e.g., age, sex, Glioblastoma (or Astrocytoma) stages, should be excluded (this information should be available in the master's table).

Please update the merged datasets (continuous and discrete) of Glioblastoma and Astrocytoma and post them here.
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Re: Merged dataset of Glioblastoma

Postby cwyoo » Thu Feb 28, 2019 1:41 pm

cwyoo wrote:
zgong001 wrote:I merged some datasets of Glioblastoma, then finally got 5754 genes and 619 subjects. The merged datasets are

GSE31545
GSE63035
GSE34824
GSE24558
GSE10878
GSE25632
GSE42670
GSE81934
GSE36245
GSE9885
GSE10878
GSE7344
GSE49822
GSE53228
GSE6014
GSE36426
GSE32374


In the merged Glioblastoma (and Astrocytoma) dataset,
* you should have a clinical variable representing Glioblastoma stages (where 0 represent normal subjects). I do not see it. In Astrocytoma dataset, Astrocytoma stages should be in the merged dataset as well.
* no missing data (I see missing data in some variables, e.g., age, sex). the GEO studies that have missing clinical variables, e.g., age, sex, Glioblastoma (or Astrocytoma) stages, should be excluded (this information should be available in the master's table).

Please update the merged datasets (continuous and discrete) of Glioblastoma and Astrocytoma and post them here.


For Glioblastoma, I suggest we prepare following six datasets (note each category has continuous and discrete datasets):

Category: Case-control (Glio-Case-Control-Continuous and Glio-Case-Control-Discrete)
Merge the following series
GSE7696
GSE6014
GSE41467
GSE36278
GSE25632
GSE10878

Category: Treatment (Glio-Treatment-Continuous and Glio-Treatment-Discrete)
Merge the following series
GSE84010
GSE7696
GSE7344

Category: Grade (Glio-Grade-Continuous and Glio-Grade-Discrete)
Merge the following series
GSE9885
GSE84010
GSE73038
GSE53228
GSE42670
GSE36426
GSE31545
GSE25632
GSE10878

Category: Survival (Glio-Grade-Continuous and Glio-Grade-Discrete)
Merge the following series
GSE84010
GSE7696
GSE42670
GSE31545
cwyoo
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Re: Merged dataset of Glioblastoma

Postby cwyoo » Thu Feb 28, 2019 1:45 pm

cwyoo wrote:
cwyoo wrote:
zgong001 wrote:I merged some datasets of Glioblastoma, then finally got 5754 genes and 619 subjects. The merged datasets are

GSE31545
GSE63035
GSE34824
GSE24558
GSE10878
GSE25632
GSE42670
GSE81934
GSE36245
GSE9885
GSE10878
GSE7344
GSE49822
GSE53228
GSE6014
GSE36426
GSE32374


In the merged Glioblastoma (and Astrocytoma) dataset,
* you should have a clinical variable representing Glioblastoma stages (where 0 represent normal subjects). I do not see it. In Astrocytoma dataset, Astrocytoma stages should be in the merged dataset as well.
* no missing data (I see missing data in some variables, e.g., age, sex). the GEO studies that have missing clinical variables, e.g., age, sex, Glioblastoma (or Astrocytoma) stages, should be excluded (this information should be available in the master's table).

Please update the merged datasets (continuous and discrete) of Glioblastoma and Astrocytoma and post them here.


For Glioblastoma, I suggest we prepare following six datasets (note each category has continuous and discrete datasets):

Category: Case-control (Glio-Case-Control-Continuous and Glio-Case-Control-Discrete)
Merge the following series
GSE7696
GSE6014
GSE41467
GSE36278
GSE25632
GSE10878

Category: Treatment (Glio-Treatment-Continuous and Glio-Treatment-Discrete)
Merge the following series
GSE84010
GSE7696
GSE7344

Category: Grade (Glio-Grade-Continuous and Glio-Grade-Discrete)
Merge the following series
GSE9885
GSE84010
GSE73038
GSE53228
GSE42670
GSE36426
GSE31545
GSE25632
GSE10878

Category: Survival (Glio-Grade-Continuous and Glio-Grade-Discrete)
Merge the following series
GSE84010
GSE7696
GSE42670
GSE31545


For Astroctytoma, I suggest we prepare following six datasets (note each category has continuous and discrete datasets):

Category: Case-control (Astro-Case-Control-Continuous and Astro-Case-Control-Discrete)
Merge the following series
GSE79122
GSE77241
GSE44971
GSE44684
GSE19728
GSE12907
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