GEO Microarray Data Cleaning

GEO Brain Tumor Microarray and RNA-seq Data Cleaning

Re: GEO Microarray Data Cleaning

Postby DanielTira » Thu Apr 05, 2018 1:16 pm

Files for GSE63669

Files removed GPL cleaning ERROR
DanielTira
 
Posts: 18
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Re: GEO Microarray Data Cleaning

Postby DanielTira » Mon Apr 09, 2018 4:13 pm

Files for GSE63669
Attachments
GSE63669aftexcel.txt
(24.5 MiB) Downloaded 134 times
GSE63669avg.txt
(12.24 MiB) Downloaded 142 times
GSE63669zscore.txt
(17.59 MiB) Downloaded 122 times
GSE63669dscrt.txt
(4.34 MiB) Downloaded 130 times
DanielTira
 
Posts: 18
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Re: GEO Microarray Data Cleaning

Postby DanielTira » Tue Apr 10, 2018 3:19 pm

Files for Super Series 62960
GSE62866
Attachments
GSE62866zscore.txt
(9.3 MiB) Downloaded 129 times
GSE62866dscrt.txt
(2.34 MiB) Downloaded 141 times
GSE62866avg.txt
(8.65 MiB) Downloaded 131 times
GSE62866aftexcel.txt
(10.78 MiB) Downloaded 125 times
Last edited by DanielTira on Tue Apr 10, 2018 3:23 pm, edited 1 time in total.
DanielTira
 
Posts: 18
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Re: GEO Microarray Data Cleaning

Postby DanielTira » Tue Apr 10, 2018 3:41 pm

Files for Super Series 62960
GSE62870
Attachments
GSE62870aftexcel.txt
(6.16 MiB) Downloaded 129 times
GSE62870avg.txt
(5 MiB) Downloaded 128 times
GSE62870dscrt.txt
(1.47 MiB) Downloaded 127 times
GSE62870zscore.txt
(5.36 MiB) Downloaded 123 times
DanielTira
 
Posts: 18
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Re: GEO Microarray Data Cleaning

Postby stefmoore » Mon May 14, 2018 1:27 pm

Files for GSE81934
Attachments
GSE81934avg.txt
(27.09 MiB) Downloaded 132 times
GSE81934dscrt.txt
(12.42 MiB) Downloaded 132 times
GSE81934zscore.txt
(56.36 MiB) Downloaded 130 times
GSE81934aftexcel.txt
(56.89 MiB) Downloaded 128 times
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Posts: 6
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Updated Version of MicroArray Cleaning Code

Postby efrain.gonzalez0 » Mon Jun 25, 2018 4:38 pm

Good evening,

I have attached the most recent version of the cleaning code to this post.

Respectfully,

Efrain Gonzalez
Attachments
RCleanDscret.txt
Cleaning Code
(13.61 KiB) Downloaded 140 times
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Re: GEO Microarray Data Cleaning

Postby brianlee » Tue Jun 26, 2018 12:09 pm

Files for GSE73038
Attachments
GSE73038aftexcel.txt
(74.32 MiB) Downloaded 129 times
GSE73038zscore.txt
(102.01 MiB) Downloaded 135 times
GSE73038dscrt.txt
(22.61 MiB) Downloaded 124 times
GSE73038avg.txt
(32.5 MiB) Downloaded 123 times
brianlee
 
Posts: 15
Joined: Fri Jun 22, 2018 3:20 pm

Re: GEO Microarray Data Cleaning

Postby brianlee » Tue Jun 26, 2018 1:40 pm

Files for GSE6014
Attachments
GSE6014aftexcel.txt
(925.45 KiB) Downloaded 130 times
GSE6014avg.txt
(508.68 KiB) Downloaded 126 times
GSE6014dscrt.txt
(374.7 KiB) Downloaded 115 times
GSE6014zscore.txt
(1.11 MiB) Downloaded 115 times
brianlee
 
Posts: 15
Joined: Fri Jun 22, 2018 3:20 pm

Re: GEO Microarray Data Cleaning

Postby JoshK » Tue Jun 26, 2018 1:43 pm

Files for GSE7696 series

GSE7696aftexcel.txt
(6.58 MiB) Downloaded 122 times

GSE7696avg.txt
(4.52 MiB) Downloaded 117 times

GSE7696dscrt.txt
(2.05 MiB) Downloaded 108 times

GSE7696zscore.txt
(8.98 MiB) Downloaded 72 times
JoshK
 
Posts: 14
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Re: GEO Microarray Data Cleaning

Postby brianlee » Wed Jun 27, 2018 11:23 am

When processing GSE42670 (GPL4091), RStudio crashes with fatal error. This occurs during step 4 of error checking (between "##Is there a clean version of the GPL file available" and "##Changing the gene ID to gene name." ).
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Posts: 15
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