Sample Sheet / Plate Layout

Samples names, dilutions and optionally groups, can be defined using an external file, either in list format or in table format.

List Format

The list format is a number of columns, with one line for each sample.   The columns are separated by commas (CSV format).    The first line contains headers.

The first column is a well name, used to identify the sample.  The second column is a name for the sample that will appear on charts and in tables.  Other columns define variables, that is, sample groupings.  A particularly important variable is Dilution, which can be used to denote positive and negative controls as well as user dilutions (see below).

For instance, a 4x3 experiment might be described as follows
    well, patientId, condition
    A01, pid1, pre-treatment	
    A02, pid2, pre-treatment
    A03, pid3, pre-treatment
    A04, pid4, pre-treatment
    B01, pid5, post-treatment
    B02, pid6, post-treatment
    B03, pid7, post-treatment
    B04, pid8, post-treatment
    C01, pid9, normal
    C02, pid10, normal
    C03, pid11, normal
    C04, pid12, normal
    C05, aneg, NA
    C06, aneg, NA
    C07, apos, NA
    C08, apos, NA
The header rows specifies that there are three columns in the file. The first two columns are always the well location and sample name.  Any number of other columns may be named, which will become named variables.  The variables can be used to pool samples across replicates, or as factors for Anova analysis.   If the fields contain commas, they must be enclosed in quotes, e.g. "Sample1,day1"

In the above example, there are 3 groups, each with 4 patients.  There are 4 other samples which are assay negative and positive controls.   They are assigned group IDs of NA, so that they are not compared to the patient groups during Anova analysis.   (Control samples would presumably always look significantly different to patient samples, and create false significance.)

The table should not be ragged; every row must have the same number of columns.
If the column has no meaningful value in that row (for instance, a negative sample is neither male nor female, neither case nor control patient) the entry should be NA, or empty.   An empty entry is denoted by two commas in immediate succession.  A space between the commas is treated as if it were a (blank) name.

Well names in the sample sheet must be unique.  Samples are matched based on the well name embedded in the FCS record for that well (A01 etc), or if there are no embedded names in the record, derived from the name of the sample.   If there were duplicates in the sample sheet, the match would be ambiguous.

The file containing this data may be either CSV or Excel format (XLSX).

Table Format

Samples names, and optionally groups, can be defined with an Excel file.   The format is best explained by example.

plate layout figure

A plate layout block begins with the keyword
The number NR defines the number of rows being described, and NC the number of columns.   The name following the semicolon identifies what is being defined.   The special name SampleName means that the block describes the names to be assigned to samples.   Another special name is Dilution, where the value is the dilution assigned to the sample.   A positive dilution, e.g. 0.25, means the sample is a positive control and the dilution is relative to the highest standard concentration.   A negative dilution, e.g. -0.25, means the sample has been diluted 4-fold before being aliquoted into the well, and the extracted protein concentration will be adjusted upward by a factor of 4 in charts and export files.

It is not necessary to define a full plate; PlateLayout(8,6);variable could define the layout of a block of 8 rows and 6 columns.

It is not necessary to enter a value in every cell.  For sample names, the sample name will revert to the cell name.   For group variables, the unassigned cells will not be included in any group.

Table format files should be in Excel format (XLSX).

Special variable names

The column (list format)  used to identify the well.  Well is always the first column in list form.   In block form the Well is implicit from position.
The block (table format) or column (list format)  used to define the short sample names shown in the Experiment table and in export files.   SampleName is always the second column in list form.
A positive dilution (e.g. 0.3333) means the sample is a positive control and the dilution relative to the highest standard concentration is 1:3
A negative dilution (e.g. -0.25) means that the in-well concentration of the sample is 1:4 diluted relative to the original stock.
A zero dilution means that the sample is a negative control, e.g. water or diluent without sample.
FCS merge
Special keywords used for Discovery panels, should not be used.

See Also


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