The following are some of the requirements that the data in your file
+ MUST fulfil before it is considered valid for this system:
+
+
+
+
File headings
+
+
The first row in the file should contains the headings. The number of
+ headings in this first row determines the number of columns expected for
+ all other lines in the file.
+
Each heading value in the first row MUST appear in the first row
+ ONE AND ONLY ONE time
+
The sample/cases (previously 'strains') headers in your first row will be
+ against those in the
+ GeneNetwork database.
+
+ If you encounter an error saying your sample(s)/case(s) do not exist
+ in the GeneNetwork database, then you will have to use the
+ Upload Samples/Cases
+ option on this system to upload them.
+
+
+
+
+
Data
+
+
NONE of the data cells/fields is allowed to be empty.
+ All fields/cells MUST contain a value.
+
The first column of the data rows will be considered a textual field,
+ holding the "identifier" for that row
+
Except for the first column/field for each data row,
+ NONE of the data columns/cells/fields should contain
+ spurious characters like `eeeee`, `5.555iloveguix`, etc...
+ All of them should be decimal values
+
decimal numbers must conform to the following criteria:
+
+
when checking an average file decimal numbers must have exactly three
+ decimal places to the right of the decimal point.
+
when checking a standard error file decimal numbers must have six or
+ greater decimal places to the right of the decimal point.
+
there must be a number to the left side of the decimal place
+ (e.g. 0.55555 is allowed but .55555 is not).
+
+
+
+
+
+
+
+
+
+
Supported File Types
+ We support the following file types:
+
+
+
Tab-Separated value files (.tsv)
+
+
The TAB character is used to separate the fields of each
+ column
.txt files: Content has the same format as .tsv file above
+
.zip files: each zip file should contain
+ ONE AND ONLY ONE file of the .tsv or .txt type above.
+ Any zip file with more than one file is invalid, and so is an empty
+ zip file.
Each of the sections below gives you a different option for data expression-data.
- Please read the documentation for each section carefully to understand what
- each section is about.
-
-
-
-
-
R/qtl2 Bundles
-
-
-
This feature combines and extends the two upload methods below. Instead of
- uploading one item at a time, the R/qtl2 bundle you upload can contain both
- the genotypes data (samples/individuals/cases and their data) and the
- expression data.
-
The R/qtl2 bundle, additionally, can contain extra metadata, that neither
- of the methods below can handle.
This feature enables you to upload expression data. It expects the data to
- be in tab-separated values (TSV) files. The data should be
- a simple matrix of phenotype × sample, i.e. The first column is a
- list of the phenotypes and the first row is a list of
- samples/cases.
-
-
If you haven't done so please go to this page to learn the requirements for
- file formats and helpful suggestions to enter your data in a fast and easy
- way.
-
-
-
PLEASE REVIEW YOUR DATA.Make sure your data complies
- with our system requirements. (
- Help
- )
-
UPLOAD YOUR DATA FOR DATA VERIFICATION. We accept
- .csv, .txt and .zip
- files (Help)
This section allows you to enter the expression data for your experiment.
+ You will need to select the species that your data concerns below.
-
samples/cases
-
-
-
For the expression data above, you need the samples/cases in your file to
- already exist in the GeneNetwork database. If there are any samples that do
- not already exist the upload of the expression data will fail.
-
This section gives you the opportunity to upload any missing samples
+
+ {%if user_aborted%}
+ Job aborted by the user
+ {%endif%}
+
+ {{errors_display(errors, "No errors found in the file", "We found the following errors", True)}}
+
+ {%if errors | length == 0 and not user_aborted %}
+
+ {%endif%}
+
+ {%if errors | length > 0 or user_aborted %}
+
+ Go back
+
+ {%endif%}
+
This feature enables you to upload expression data. It expects the data to
+ be in tab-separated values (TSV) files. The data should be
+ a simple matrix of phenotype × sample, i.e. The first column is a
+ list of the phenotypes and the first row is a list of
+ samples/cases.
+
+
If you haven't done so please go to this page to learn the requirements for
+ file formats and helpful suggestions to enter your data in a fast and easy
+ way.
+
+
+
PLEASE REVIEW YOUR DATA.Make sure your data complies
+ with our system requirements. (
+ Help
+ )
+
UPLOAD YOUR DATA FOR DATA VERIFICATION. We accept
+ .csv, .txt and .zip
+ files (Help)