Frequently Asked Questions (FAQ)

If you cannot find the answer to your question in this FAQ or other ArrayExpress help pages then please email us at miamexpress@ebi.ac.uk.

The FAQ is divided into 3 sections:

  1. Using ArrayExpress
  2. Submitting data to ArrayExpress (general)
  3. Submitting data to ArrayExpress (MIAMExpress-specific questions)

 

1. Using ArrayExpress

Searching and understanding data

 

Data access policy - permissions and restrictions
FTP data download and programmatic access
Other general questions

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2. Submitting data to ArrayExpress (general)

Accession numbers
Keeping unpublished data private
Public release date
Which files to submit
Making changes to data already submitted to Arrayexpress

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3. Submitting data to ArrayExpress (MIAMExpress-specific questions)

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1. Using ArrayExpress

Searching and understanding data
  • How do I search the ArrayExpress database?
    For simple keyword searches and browsing, please visit the search help page. For more complex search queries, e.g. "Find me all the microarray experiments on Agilent chip X studying diabetes in mouse", please refer to the advanced search help.
  • How do I link sample and data file information in the downloadable files?
    All the downloadable files relating to an experiment are in MAGE-TAB format. Top level information about an experiment (title, authors, protocols etc) is in a file called the IDF (Investigation Definition Format). Sample, extract and hybridization information is in a file called the SDRF (Sample and Data Relationship Format) which also links to the protocol information in the IDF. The SDRF lists which data files are associated with each hybridization or scan. For more information on the MAGE-TAB format, please visit the MAGE-TAB help page.. The IDF and SDRF components are described in greater detail on this help page.
  • I read a paper that referred to data in ArrayExpress but when I searched for the data I got no hits. Why?
    It could be that the submitter of the data has not yet told us that the experiment should be made public. If you come across this problem please email us at - tell us which paper you found the reference in and the ArrayExpress accession number quoted if any. We will make this data publicly available.
  • I have seen ArrayExpress experiment accessions with prefixes such as "E-MEXP", "E-MTAB", etc. What do the prefixes mean?
    The prefixes indicate the source and/or submission route from which the data came from. The common ones are:
    • MEXP = data submitted via the MIAMExpress submission route
    • TABM = data submitted via the Tab2MAGE submission route (discontinued since January 2012)
    • MTAB = data submitted via the MAGE-TAB submission route
    • GEOD = data imported from NCBI Gene Expression Omnibus
    See the accession codes help page for more information.

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Data access policy - permissions and restrictions
  • Are there any restrictions on the use of microarray data obtained through ArrayExpress?
    No restrictions, all public data from ArrayExpress can be used by anyone and our services are completely free of charge.
  • Do I need a login account to view or access data in ArrayExpress?
    For public data, no. We only provide login accounts to data submitters so that they, and their reviewers, can access pre-publication private data. All other data can be viewed by everyone.
  • I've lost my ArrayExpress website login details. What do I do?
    If you are viewing a curated experiment which you submitted to ArrayExpress, use the forgotten password reminder form in the login box. If you are not the data submitter (e.g. a reviewer), then please contact the the submitter. We can only give ArrayExpress login details to the owners of the data directly.
  • I'm reviewing a paper. How do I get a login to view private data that the authors have deposited in ArrayExpress?
    Reviewer login details are sent to submitters on completion of the processing of their submission. Please contact the data submitter, via the journal editor, to request this login information. We cannot provide access to private data to anyone without first getting authorization from the submitter or journal.

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FTP data download and programmatic access
  • Is there an FTP site to download data files in bulk?
    Yes, all the data and array designs in ArrayExpress are available for direct download in a number of different formats. For more information on what files are available and how to access them see our FTP files for download help.
  • Do you have any application programming interfaces (APIs) for accessing ArrayExpress?
    Yes, we have REST-style and WebService APIs for accessing ArrayExpress. Details can be found here: Programmatic access.
Other general questions
  • How much overlap is there between ArrayExpress and the NCBI Gene Expression Omnibus (GEO)?
    We import data on a weekly basis from NCBI Gene Expression Omnibus (GEO). All experiments imported from GEO have accession numbers in the format of E-GEOD-n, where n is a number. For example, GEO accession "GSE29080" would become "E-GEOD-29080" in ArrayExpress. For more information see the GEO data import page.
  • How do I cite ArrayExpress in my publication?
    You should include your experiment accession number and the URL to ArrayExpress home page, www.ebi.ac.uk/arrayexpress. e.g. "Microarray data are available in the ArrayExpress database (www.ebi.ac.uk/arrayexpress) under accession number E-MEXP-12345." If you wish to include a citation for ArrayExpress then the following publication should be used: Rustici.G et al. 2013 ArrayExpress update - trends in database growth and links to data analysis tools. Nucleic Acids Res, doi: 10.1093/nar/gks1174. Pubmed ID 23193272.

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2. Submitting data to ArrayExpress (general)

Accession numbers
  • I urgently need an accession number to include in my publication - how can I get one?
    Firstly, start your ArrayExpress submission if you have not already done so! ArrayExpress does not provide accession numbers in advance of submission of data. This is in line with the NCBI Gene Expression Omnibus (GEO)'s policy of provision of accession numbers after deposition. If you have completed the submission and are waiting for a response you can email us at to let us know how urgently the accession number is required. To help us find your submission tell us your username, the name of the experiment or array and if you submitted via the MIAMExpress or MAGE-TAB submission route. We will reply to your email as quickly as possible but please note that we often have several submissions requiring urgent attention.
  • How long will it take to get an accession number?
    After you complete a submission it is put in a queue awaiting initial review and checking. If there are no major problems then your submission will be assigned to a curator who will look into the details of your submission to make sure everything is indeed in good order. If there are no problems at all, we will send you the accession number, otherwise we will contact you to advise on how to revise and resubmit before an accession number is assigned. It is therefore important that you include as much meta data as possible in your submission to speed up the curation process. We aim to respond within a week upon receiving the submission, but response times do vary depending on submission volume, so please bear with us.

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Keeping unpublished data private
  • Can my data be kept private after I submit it?
    Yes, all submitted information will be kept private until the release date that you set at the time of submission, or until a publication is released that contains the ArrayExpress accession number relating to your data. Please see our data availability page for more information.
  • The journal I am submitting to have requested private access to my data - how do I get an ArrayExpress login for them?
    Firstly, start your ArrayExpress submission if you have not already done so! You will be sent login details for viewing your private data on the ArrayExpress website only at the end of the curation process, i.e. after your data has been loaded into the ArrayExpress database. If you are really pushed for time, reply to the email thread sent to you by the ArrayExpress curator in charge of your submission, or email us at to let us know about your situation. We will try our best to fast-track your submission.
  • I tried to login to ArrayExpress to see some recently submitted private data but it said my username and password were invalid. Why?
    Possibly you have tried to login with your MIAMExpress or MAGE-TAB submitter account. These "submitter" accounts can only be used for submitting data, not viewing it in ArrayExpress. We will provide you with an ArrayExpress login account after your submission has been curated and then loaded into ArrayExpress. If you are using an ArrayExpress login which you have just received, it might not be working yet because ArrayExpress is updated only once a day at about 06:00 GMT. Try again after this time. If it still does not work contact us at and tell us what login details you are trying to use and which page you tried those details on.

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Public release date
  • I don't know when my paper will be published so what should I put as the release date?
    Enter an estimated public release date up to 1 year in the future from the day of submission. You can email us at at any time to request a change to the release date and you'll be sent a reminder email one month before release is due. Please see our data availability page for more information.
  • My paper is about to be published - how do I make the data public?
    Email us at with the experiment accession number and tell us when it should be made public. Please send us the citation information, including PubMed ID and Digital object identifier (DOI) too so we can add this to your experiment's record. Please see our data availability page for more information.

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What files to submit
  • Is there any software I can use to create a template spreadsheet of my experiment data for submission?
    Yes. Using the MAGE-TAB submission tool, you can generate a template spreadsheet specific to your experiment. Upon logging in the tool, you will first create an experiment and then select some terms (e.g. species, experiment design, sample attributes) which are relevant to your experiment from a series of drop-down lists. Once you've saved your selection, you will be given the "generate template" option, which generates a spreadsheet pre-filled with some information and column headings relevant to your experiment. Check out our MAGE-TAB quick start submission guide or YouTube video to see how the submission tool works. Once you have the spreadsheet, you should fill in the empty fields with specific information, e.g. sample names, raw data filenames, etc.
    There are also some third party data annoation tools that can generate MAGE-TAB spreadsheets for you for uploading through the MAGE-TAB spreadsheet submission tool. There is more information about them here.
  • Which files do I need to submit for an Affymetrix experiment?
    For a MIAME compliant submission we need Affymetrix .CEL files as raw data and some form of processed, probe set level data. The processed data is preferably a matrix file generated by software such as as robust multi-array average (RMA) or dChip. A matrix file has the Affyemtrix probesets in the rows and processed intensity values per hybridisation in the columns. If you do not have such a matrix file, we also accept Affymetrix .CHP files if you have them. For more information on how to format your processed matrix data files see our MIAMExpress data file help page if you are submitting using MIAMExpress, or MAGE-TAB data matrix example if you are using MAGE-TAB.
  • How do I submit an Illumina experiment?
    Illumina experiments must be submitted using our spreadsheet submission route: MAGE-TAB. For Illumina experiments you do not need to submit data for every spot on the array. Please use the Illumina GenomeStudio software (previously known as the "BeadStudio" software) with the 'ArrayExpress Data Submission Report Plug-in' to generate the raw data file for submission. The plug-in is available from the Illumina connect website. Please take a look at this example Illumina raw data file. The unique identifiers in the raw data file should be taken from the "PROBE_ID" column of the GenomeStudio-generated file. (Note: the Illumina GenomeStudio-generated file would have column headings "PROBE_ID" and "ProbeID", and they are not the same!) For the processed data, a data matrix is preferred (PROBE_IDs in rows, processed measurements per hybridisation in columns), as in this MAGE-TAB matrix file example.
  • How do I submit a high throughput sequencing (HTS) experiment?
    High throughput sequencing gene expression data should be submitted using the MAGE-TAB spreadsheet submissions system. You will need to provide as much information as possible about the starting materials (samples) and protocols used, raw sequence data files for each sample and optionally processed data files, e.g. expression values or SNP calls linked to genome coordinates. Raw data files must be in a format accepted by the Sequence Read Archive (SRA) at the European Nucleotide Archive (ENA), otherwise we will not be able to process your submission. We strongly recommend that you check out our sequencing submissions help page as it explains the requirements in a lot more detail.
  • I have very large data files, do I need to upload them through the web interface?
    Large data files can be submitted to us via FTP instead of uploaded through the MAGE-TAB submission web form. One small size data file must also be uploaded through the web form to allow the submission to be completed. This file will be ignored if it is not listed in the MAGE-TAB spreadsheet. Please email us at miamexpress@ebi.ac.uk to let us know if you have FTPed the files. If you are submitting through MIAMExpress please email us at miamexpress@ebi.ac.uk about how to proceed with your submission.
  • I have MAGE-ML files generated from in-house pipelines. Does ArrayExpress still accept them?
    No. MAGE-ML files are no longer supported and accepted by ArrayExpress. Please submit your array design files and/or experiment data using MAGE-TAB. You can find out more about MAGE-TAB submissions in this MAGE-TAB submission tutorial. If you would like to update your pipeline to generate MAGE-TAB files, please write to us at miamexpress@ebi.ac.uk and we will try our best to offer assistance.

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Making changes to data already submitted to ArrayExpress

  • I hit "Submit Experiment" (MAGE-TAB route) / "Complete Submission" (MIAMExpress route) at the end of my submission but I haven't actually finished editing. I logged in to the submission tool but can't see my experiment anymore - what should I do?
    Email us at miamexpress@ebi.ac.uk as soon as possible and ask us to "reopen" the submission. (Your submission is considered "closed" once it has reached the hands of a curator, so as to avoid confusing, concurrent editing of the same submission by the submitter and curator.) To help us find your submission tell us your username, the experiment or array name and if you used the MIAMExpress or MAGE-TAB submission route.
  • My data has been loaded into ArrayExpress but I need to change/correct something - how do I do this?
    Email us at miamexpress@ebi.ac.uk with the accession number and describe what corrections you would like to make. Minor corrections such as fixing typing errors can be made easily. Major changes like adding or removing hybridizations usually require the experiment to be unloaded from the ArrayExpress database, edited, re-curated and reprocessed, which can take some time. Please see our data availability information page for more information.
  • My contact details have changed, how do I update them?
    Send your new contact details to us at miamexpress@ebi.ac.uk and we will change them in ArrayExpress.

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3. Submitting data to ArrayExpress (MIAMExpress-specific questions)

  • I've logged in to MIAMExpress but I get an error that says "Unfortunately you can not continue working with this tool", what's wrong?
    This error message appears if you have used the wrong casing in your username or password when logging in. Both the username and password are case sensitive. Email us at miamexpress@ebi.ac.uk if you need a reminder of your login details.
  • I've just submitted a custom array design to MIAMExpress but I can't see it on the list of array designs in my experiment submission - where is it?
    New array designs that have not yet been processed can be found at the end of the list of array design names so start at the bottom and you should see it.
  • I have submitted my protocols using MIAMExpress, where do I upload the data?
    Go back to the 'Submission types' page using the link in the navigation bar at the top of the protocol submission page. Select 'Experiment submission' and submit your data either by clicking the "Start or edit an experiment submission" link to launch the batch upload tool, or by using the webform interface. There is more information on the batch loader help page and MIAMExpress help page.

    Navigation link to submission types

    Experiment submission choices

  • I've described my experiment and my samples using the MIAMExpress webform but I have many samples and would like to do batch upload of data files. How do I do that?
    You can do this by using the MIAMExpress batch upload tool. To use this tool, first save the information you have already entered on the form by clicking at the "Submit" button at the bottom of the form. (This will not submit data for curation but will submit the information to be stored in a database.) Next, return to the 'Experiment submissions' page (there is a link to this on the navigation bar at the top of all MIAMExpress web pages), and click the "Start or edit an experiment submission" link (see screenshot in question above). When you login to this tool you'll be able to see the experiment you've started and won't lose any of the information you've already entered. See the batch loader help page for full instructions. (If you change your mind and prefer the webform instead, please see the web form interface help page for instructions on how to complete the submission in the web interface).
  • My normalized data is in a single "Combined data file" but when I select my normalization protocol I get errors saying I have to upload separate normalized files for each hyb. Help!
    Don't select a normalization protocol in your experiment submission. You need to create a transformation protocol, instead of a normalization protocol, to describe the single normalized data file. To do this, after the hybridizations page, upload the single normalized file, at which point you can link the single normalized file to a transformation protocol.
  • Where do I upload my single "Combined data file" containing processed data from all hybs ?
    It happens at the very last stage of the submission process, after you have created all hybridisations and uploaded raw data files. Therefore, please upload all you raw data for the hybridizations first. If MIAMExpress complains that you have not uploaded normalized data at this stage it is because you have a normalization protocol selected so unselect this protocol. To proceed to the very last stage of the submission process, click the submit button on the hybridizations tab in the batch upload tool (or, in the web forms, return to the 'create hybridizations' page and click the continue button at the end of the page). You will then be taken to a form where you can upload your "Combined data file" and select the transformation protocol describing how it was generated.

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