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EBIArrayExpressFAQ

ArrayExpress FAQ

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

 

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ArrayExpress submission FAQ

 

General Questions

  1. I urgently need an accession number to include in my publication - what should I do?
    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 GEO 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 used MIAMExpress, Tab2MAGE or MAGE-TAB. We will reply to your email as quickly as possible but please note that we often have several submissions requiring urgent attention.
  1. 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 send you the accession number. If there are problems we will contact you and ask you to resubmit before an accession number is assigned. Either way we aim to respond within a few days but response times do vary depending on submission volume.
  1. 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. For more information on our data release policy see the ArrayExpress submission help page.
  1. 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. You can email us at at any time to request a change to the release date and you'll be sent a reminder email 1 month before release is due. For more information on our data release policy see the ArrayExpress submission help page.
  1. What files do I need to submit for an Affymetrix experiment?
    For a MIAME compliant submission we need Affy .CEL files as raw data and some form of processed, probe set level data. The processed data could be the Affymetrix .CHP files or data from some other software such as as RMA or dChip. For more information on how to format your processed data files see our data file help page. You do not need to provide CHP files if you did not use them. Affymetrix .EXP files can be provided but they are not mandatory as the Affy software no longer creates them.
  1. How do I submit an Illumina experiment?
    Illumina experiments must be submitted using one of the two spreadsheet sheet submission routes: Tab2MAGE or MAGE-TAB For Illumina experiments you do not need to submit data for every spot on the array. Please provide the tab delimited text file generated by BeadStudio containing data for each PROBE_ID as your raw data. Illumina have recently released the 'ArrayExpress Data Submission Report Plug-in' for BeadStudio which will generate a raw data file plus a basic Tab2MAGE spreadsheet for you to fill in with your experiment and sample information. This plug-in is available from the downloads section of the Illumina iCom website. There is more information on supported Illumina data files in the Tab2MAGE documentation.
  1. How do I submit a high throughput sequencing experiment?
    High throughput sequencing gene expression data should be submitted using the MAGE-TAB spreadsheet submissions system. You will need to provide information about the samples and protocols used, trace data files for each sample and processed data files in which expression values are linked to genome coordinates for example. See the UHTS submissions help page for more information.
  1. I hit submit at the end of my submission but I need to make some changes - what should I do?
    Email us at as soon as possible and ask us to reopen the submission. To help us find your submission tell us your username, the experiment or array name and if you used MIAMExpress, Tab2MAGE or MAGE-TAB submission routes.
  1. The journal I am submitting to have requested private access to my data - how do I get an ArrayExpress login for them?
    You will be sent ArrayExpress login details for viewing your private data at the end of the curation process after your data has been loaded into ArrayExpress. It can take some time to load an experiment into ArrayExpress - experiments with many large data files take longest. If you urgently need reviewer login details we can set up an account in advance but the reviewers will not be able to see the data until it has finished loading into ArrayExpress. Ask the curator dealing with your submission if you would like a reviewer login to be set up in advance.
  1. I tried to login to ArrayExpress to see some recently submitted data but it said my username and password were invalid. Why?
    Possibly you have tried to login with your MIAMExpress or spreadsheet submitter account. These 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 6am 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.
  1. My contact details have changed, how do I update them?
    Send your new contact details to us at and we will change them in ArrayExpress.
  1. 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 and PubMed ID too so that we can add this to your experiment.
  1. My data has been loaded into ArrayExpress but I need to change/correct something - how do I do this?
    Email us at with the accession number and describe the type of correction you need 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 and reprocessed which can take some time.
  1. Is there any software I can use to create a spreadsheet of my experiment data for submission?
    Using the MAGE-TAB spreadsheet submission route, you can generate a template spreadsheet specific to your experiment by first creating an experiment and then selecting the 'generate template' option. The spreadsheet is then filled out with information relevant to your experiment (description, protocols, sample information etc) and then uploaded along with your data files through the MAGE-TAB spreadsheet submission web page. 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 web page. There is more information about them here.

 

 

MIAMExpress specific questions

  1. I’ve logged in to MIAMExpress but I'm getting 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 if you need a reminder of your login details.
  1. I have submitted my protocols using MIAMExpress, where do I upload the data?
    Go back to the 'Submission types' page (there's a link to it on the navigation bar at the top of the protocol submission page). Select 'Experiment submission' and launch the batch upload tool to start an experiment submission. There is more information on the MIAMExpress help page.
  1. I've described my experiment and my samples, where do I upload the data?
    You are probably using the old MIAMExpress web form interface. An easier way to use MIAMExpress is with the new batch loader tool. To use this tool 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 launch batch loader link. 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. (see the web form interface help page for instructions on how to complete the submission in the web interface).
  1. 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.
  1. My normalized data is in a single combined file but when I select my normalization protocol I get errors saying I have to upload separate normalized files for each hyb. Help!
    You need to create a transformation protocol, instead of a normalization protocol, to describe the single normalized data file. Don't select a normalization protocol in your experiment submission. After the hybridizations page you'll be asked to upload the single normalized file and link to your transformation protocol.
  1. Where do I upload my single combined file containing data from all hybs (final gene expression matrix)?
    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. After selecting all the raw data files 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 final gene expression matrix and select the transformation protocol describing how it was generated.

 

ArrayExpress Experiment Archive FAQ

  1. 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.
  1. How much over-lap is there between ArrayExpress and the Gene Expression Omnibus (GEO)?
    We import data on a weekly basis from GEO (NCBI). As a priority all GEO experiments which are in GEO datasets on catalogue Affymetrix and Agilent platforms are imported and we re-curate these before loading into ArrayExpress. We also import all GSE on these platforms and these are loaded uncurated if they pass our quality checks (e.g. no corrupt data files). All experiments imported from GEO have accession numbers in the format of E-GEOD-n, where n is a number. For more information see the GEO data import page.
  1. 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: Parkinson et al. 2008 ArrayExpress update—from an archive of functional genomics experiments to the atlas of gene expression. Nucl. Acids Res., doi:10.1093/nar/gkn889. Pubmed ID 19015125.
  1. Do I need a login account to view data in ArrayExpress?
    No. We only provide login accounts to data submitters so that they, and their reviewers, can access pre-publication data. All other data can be viewed by everyone.
  1. I’m reviewing a paper but I haven't been given a login to view private data that the author's have deposited in ArrayExpress. How can I get one?
    Reviewer login details are sent to submitters on completion of the processing of their submission. Please contact the data submitter, via the journal, to request this login information. We cannot provide access to private data to anyone without first getting authorization from the submitter or journal.
  1. I've lost my ArrayExpress login details. What do I do?
    If you are the data submitter then email us at for a reminder – tell us the accession number of the experiment you want to view. If are not the data submitter then please contact them. We can only give ArrayExpress login details to the owners of the data directly.
  1. 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 this 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.
  1. I don't understand how to link the sample and data file information in the files I have downloaded for an experiment. Can you explain how to do this?
    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 links to the protocol information in the IDF. The SDRF also lists which data files are associated with each hybridization or scan. The MAGE-TAB format is described on the MAGE-TAB help page. More detailed information about the MAGE-TAB format can be found here.
  1. I downloaded a data file from ArrayExpress but it is too big to open, what can I do?
    You can choose to download just a subset of the data from an experiment by using the 'retrieve data' page in the advanced query interface. You can get to this page by following the 'view detailed data retrieval page..' link from your experiment search results. There is help on how to use the retrieve data page here: Retrieve data page help.
  1. Is there a standard URL format for linking to an experiment in ArrayExpress?
    Yes, you can link to an experiment using its accession number e.g. to retrieve information about experiment E-MEXP-700 use this link: http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-700
  1. Do you have any APIs for accessing ArrayExpress automatically?
    Yes, we have REST-style and WebService APIs for accessing the ArrayExpress experiment archive and Gene Expression Atlas. Details can be found here: Programmatic access.
  1. Do you offer 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.
  1. I am using the ArrayExpress Bioconductor package to download data but it doesn't recognize the data file archive names?
    We recently (October 2009) changed the naming convention used for the raw and processed data file archives to split very large archives into several smaller ones. The archive names now contain a sequence number after the words 'raw' or 'processed' e.g. E-MEXP-568.raw.1.zip. Older releases of the ArrayExpress package from Bioconductor do not support this naming convention. Please use the latest version (1.6.0) which is available from the Bioconductor site http://bioconductor.org/packages/release/bioc/html/ArrayExpress.html

 

ArrayExpress Atlas FAQ

See the Atlas-specific FAQ page.

 

 

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