Validate your experiment submission

You must validate your submission before submitting for curation. The validation step aims at catching errors such as missing mandatory information (e.g. public release date, library preparataion protocol for a sequencing experiment, some samples have not been assigned any raw or processed data files), or inconsistencies in your submission (e.g. for a two-colour microarray experiment, a hybridisation assay is associated with one labeled extract only but not two). Having errors like these caught and fixed before submission allows us to process your experiment faster for loading into ArrayExpress.

The checks will be run when you click Validate. It should only take a few seconds:

validate

 

If there are no errors, you'll see a message: Validation has been successful and you can proceed to submit the experiment to ArrayExpress.

If however there are errors, they will be listed like this:

validate message

Errors must be fixed before submission. Here are some common errors and how to fix them:

I want to submit an experiment

Common errors and fixes

If you're submitting a two-color microarray experiment, some of the error messages referring to labels or assays may be caused by small inconsistencies in how you assigned labels to samples, or files to samples. This page shows an example on how to construct a two-colour experiment, which you may find useful.

If you need further help with fixing errors, please email us at annotare@ebi.ac.uk, citing your submission login email, experiment title, and the error message(s) triggered. A curator will investigate and suggest solutions.

Error Fix
An experiment must have at least one experimental variable specified An "experimental variable" is the main variable under investigation, often related to the hypothesis or intent of the experiment.

For example, for an experiment comparing wild-type against knock-out samples, attribute "genotype" should be included (to indicate which samples are wild-type and which are knock-out), and the attribute should be indicated as an "Experimental Variable". Likewise, "compound" would be an "experimental variable" for an experiment comparing samples treated with some drugs/chemicals against untreated controls.

See the Describe your samples and data files - Specify sample attributes section for more details.
NOMINAL_LENGTH must be a positive integer and NOMINAL_SDEV must be a positive number for paired-end sequencing samples in the ENA library info Nominal length is the expected size of the sequenced insert in the library, and Nominal SDev is the standard deviation of the Nominal length. See the Describe your samples and data files - Create extracts and assign ENA library info section for more details.
At least one protocol must be used in an experiment Protocols describe the wet-lab and dry-lab (computational) procedures carried out in your experiment, e.g. how the starting materials were grown/sourced/treated, DNA or RNA extraction, data processing steps etc. To process your submission we require details of the protocols used. See the Describe your samples and data files - Protocols section for more details.
A raw data file name must only contain alphanumeric characters, underscores and dots File names such as "my file (1).txt" can confuse Annotare processing pipeline since whitespaces, some punctuations and symbols such as brackets could be accidentally misinterpreted as part of the processing code. So instead of "my file (1).txt", please use filenames such as "my_file_1.txt" or "myfile.1.txt" instead. In Annotare, in the Upload and assign files section, on the left pane where you've uploaded files either directl or via FTP, you can rename any uploaded file by double-clicking at the file name.
For an array assay (microarray experiment) the associated labeled extract(s) must have distinct labels
OR
Name of an array data matrix node must be valid file location
These errors are often triggered when the data file type (raw, raw matrix, processed or processed matrix) chosen does not match the actual content of your uploaded files, e.g. when "processed matrix" type is selected where in fact per-sample processed files (i.e. non-matrix) are provided. The file types are explained further on help page What format should my microarray data files be in?. Make sure you've selected the correct file type.
At least one contact must have 'submitter' role specified When creating a contact, make sure you assign a role to it. At least one of the contacts created must have the role 'submitter', whose name and email address will be displayed in the "Contact" field of an ArrayExpress record (here is an example). See the Describe your experiment - Contacts section for more details.
For an array assay (microarray experiment) the associated labeled extract(s) must have distinct labels. If you're submitting a two-color microarray experiment, the chance is that you have accidentally assigned wrong labels to your samples when creating labeled extracts, or accidentally assigned wrong files to the wrong sample. See the Describe your samples and data files - Create labeled extract and assign a label (two color only) section for more details.
A source (starting sample for the experiment) must have an 'Organism' characteristic specified "Organism" is a mandatory attribute when descrbing your samples. Please provide details of the organism used in the "Samples and Data" tab. Choose the Latin name of your species from the drop-down list under "Organism". If your organism is not in the drop-down list, please email us at annotare@ebi.ac.uk.