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Error messages

There are three types of error messages in TMA Navigator: upload, analysis and system.

Upload errors are issues with the input data itself - for example, if it isn't formatted correctly, or if batch correction is requested but the data's experimental design means that batch correction isn't possible. Upload errors can usually be corrected by making changes to the input file and re-uploading.

Analysis errors may arise due to particular aspects of the uploaded data - some analyses can't be applied to certain kinds of data. For example, a Kaplan-Meier survival plot on categorical data requires at least two different scores for the marker examined (it is not possible to stratify samples which all have the same score).

System errors are related to our computing systems and are not correctable by the user. We strive to keep TMA Navigator bug-free, but if you believe you've discovered a bug, please first check it isn't a validation or analysis error as described below, and contact us with details so we can get it fixed as soon as possible. More information on submitting error reports can be found in the System errors section at the bottom of this page.

[Top]Upload errors

Upload errors include issues such as input data being in an incompatible format, invalid input data (such as non-numerical protein scores) or problems occurring during batch correction

Validation errors with TMA or survival data

Please consult the help sections on the TMA data requirements and the survival data requirements. Follow the instructions in any error messages to make your data compatible. Most corrections are straightforward - for example, removing non-ASCII characters from marker identifiers.

Validation error during batch correction

This error may occur if all samples (rows in the input data) have more than 80% missing values. In our experience more than 80% missing data makes it difficult to successfully perform ComBat batch correction [Johnson et al. 2007 Biostatistics 8:118]. This error is also returned if batches are confounded with covariates when applying batch correction. To understand what this means, look at the table below.

*Batch*covGender
1Male
1Female
1Male
2Female
2Female

In the table above, there are no male patients in batch 2. This means that there's no way to identify whether variation in the batch 2 patients is a genuine batch effect or due to gender. This is a limitation in the experimental design - the only way to work around this issue is either to remove gender as a covariate (and hence assume variation is due to batch rather than gender), or disable ComBat batch correction. More discussion around issues with batch correction can be found on the ComBat user forum and in Johnson et al. Biostatistics 8:118.

Import error

This error occurs if there has been a problem with the upload that isn't covered by the above two headings, in this case please contact us with the details, being sure to include the URL of the page which generated the error and any error messages that you received.

[Top]Analysis errors

The sections below gives information on errors that may occur when attempting to run analyses in TMA Navigator:

Mixture model plots

Mixture model plots are not always generated for every marker. Our approach to mixture modelling requires at least nine score values, therefore markers with fewer than nine unique values are skipped.

Kaplan-Meier (mixture model) plots

Kaplan-Meier plots are not always generated for every marker (typically a protein). A marker is skipped if either a mixture model was not generated (see section on mixture model plots, above) or more commonly, the resulting mixture model only has one group - Kaplan-Meier plots require at least two groups in order to compare survival and generate statistics, so single group (unimodal) models are necessarily skipped. Additionally, a Kaplan-Meier plot is not generated where there are fewer than 10 samples with scores for the marker (protein) and available survival data.

Kaplan-Meier (tertile) plots

Kaplan-Meier plots are not always generated for every marker (typically a protein). A marker is skipped if it has only one distinct score value, as samples are therefore not separable into multiple groups. There must also be at least 10 samples with scores defined for the marker who also have survival information present.

Kaplan-Meier (categorical) plots

Kaplan-Meier plots are not always generated for every marker (typically a protein). A marker is skipped if it has only one distinct score value, as samlpes are therefore not separable into multiple groups. There must also be at least 10 samples that have scores defined for the marker and survival data.

Networks

Networks require that at least 10 samples have scores specified for every marker (i.e. have no missing values). If this requirement is not met, a network will not be generated. If the dataset contains a large number of markers, it may be worth considering removing some markers (e.g. those with the most missing data) until the requirement of 10 fully specified samples requirement is met.

[Top]System errors

If you have received an error message from TMA Navigator, or have found something that isn't working as expected, please consult the validation and analysis error messages above to make sure it isn't an issue with the dataset itself. If you have found an issue that isn't covered, please report this on the contact form including the details, being sure to let us know the URL of the page which generated the error and to give any error messages that you received. We appreciate your feedback and will get back to you as soon as possible.

[Top]Requirements

TMA Navigator has been verified to work successfully in all major web browsers. The following list includes browser versions which have been extensively tested, although the site should work in all modern browser versions. However, if you are having trouble with the service, we recommend using one of the versions listed, if possible.

Please note that Javascript must be enabled in your web browser. Javascript is a browser feature which is normally enabled by default. Please see your browser's documentation or contact your organisation's IT support team, if applicable, for further information.

The Adobe Flash plugin is required to view networks in the web browser.

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