Array Express experiment

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[[Category:Import Expression Data]]
 
[[Category:Import Expression Data]]
  
Array Studio allows the user to add ArrayExpress data from within the program itself. Rather than having to individually download data, sample information, and annotation, Array Studio will perform this automatically.
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OmicSoft Studio allows the user to add processed ArrayExpress microarray data from within the UI. Rather than having to individually download data, sample information, and annotation, OmicSoft Studio will perform this automatically.
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{{Tips|This function only works for microarray data, because it relies on the '''Array Design REF''' column in the SDRF. RNA-seq data do not require this metadata column.}}
  
 
Selecting ''ArrayExpress Experiment'' in the Specify Expression Data Source window and click OK to open the ArrayExpress Archive window. This takes the user to an internal web browser sent directly to the EMBL-EBI website.
 
Selecting ''ArrayExpress Experiment'' in the Specify Expression Data Source window and click OK to open the ArrayExpress Archive window. This takes the user to an internal web browser sent directly to the EMBL-EBI website.
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The user can search for a dataset on the web page. Once they have identified a dataset of interest, entering the identifier into the ArrayExpress experiment ID box and clicking Display Page. If confirmed, the user can select Download Data which will automatically download the data, annotation, and sample information for the public dataset. This will be added as a new dataset in the Project Explorer.
 
The user can search for a dataset on the web page. Once they have identified a dataset of interest, entering the identifier into the ArrayExpress experiment ID box and clicking Display Page. If confirmed, the user can select Download Data which will automatically download the data, annotation, and sample information for the public dataset. This will be added as a new dataset in the Project Explorer.
  
 
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==Common Errors==
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A variety of issues with the data submission can prevent the importation of data, including non-standard matrices exported from analysis programs with additional headers, missing processed data, or RNA-seq data.
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===Processed data file can not be downloaded for experiment===
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This error message generally means that the data submission does not include a "Processed data" file, so there is nothing to import from this function. We recommend downloading the data from the web site, then importing the CEL files.
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e.g. [https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-9080/]
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===Array Design REF can not be found===
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NGS submissions do not require the column "Array Design REF", so this function will not import the data matrix. We recommend either downloading the matrix and importing it and the design file into OmicSoft Studio with [[Import_Expression_Data|Tab-delimited file]], or downloading the BAM files and importing or re-aligning.
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e.g. [https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-9163/]
 
== OmicScript ==
 
== OmicScript ==
 
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Latest revision as of 15:34, 29 June 2020


OmicSoft Studio allows the user to add processed ArrayExpress microarray data from within the UI. Rather than having to individually download data, sample information, and annotation, OmicSoft Studio will perform this automatically.

Tips.pngThis function only works for microarray data, because it relies on the Array Design REF column in the SDRF. RNA-seq data do not require this metadata column.


Selecting ArrayExpress Experiment in the Specify Expression Data Source window and click OK to open the ArrayExpress Archive window. This takes the user to an internal web browser sent directly to the EMBL-EBI website.

ArrayExp0.png

The user can search for a dataset on the web page. Once they have identified a dataset of interest, entering the identifier into the ArrayExpress experiment ID box and clicking Display Page. If confirmed, the user can select Download Data which will automatically download the data, annotation, and sample information for the public dataset. This will be added as a new dataset in the Project Explorer.

Contents

Common Errors

A variety of issues with the data submission can prevent the importation of data, including non-standard matrices exported from analysis programs with additional headers, missing processed data, or RNA-seq data.

Processed data file can not be downloaded for experiment

This error message generally means that the data submission does not include a "Processed data" file, so there is nothing to import from this function. We recommend downloading the data from the web site, then importing the CEL files. e.g. [1]

Array Design REF can not be found

NGS submissions do not require the column "Array Design REF", so this function will not import the data matrix. We recommend either downloading the matrix and importing it and the design file into OmicSoft Studio with Tab-delimited file, or downloading the BAM files and importing or re-aligning. e.g. [2]

OmicScript

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