LabKey Server understands and processes Excel files of Luminex® results that have been output by a Bio-Plex instrument's software
for Luminex experiments. You can see an example Excel file here
. This page reviews the Excel file format.
Microsoft Excel files in *.xls (1997-2003) and *.xlsx (2007-2013) formats are supported; Microsoft Excel *.xls 95/5.0 format is not supported.
LabKey Server's Luminex features have been tested using data for 96-well plates, but are expected to work for 384-well plates as well. The larger plates are used by newer instruments that allow multiplexing of up to 500 analytes in each well. Devices that only support 96-well plates are usually limited to a maximum of 100 analytes in each well.
- The file is typically a multi-sheet workbook
- Each spreadsheet (tab) in the workbook reports data for a single analyte. One sheet may report measurements for the blank bead.
- Each sheet contains:
- A header section that reports run metadata (see below for details)
- A data table that reports values for wells
- A footer section that describes data flags and shows curve fits equations and parameters
Run Metadata in the Header
Most of the metadata fields reported in the file header are imported as "Excel File Run Properties." With the exception of Analyte
, all of these metadata properties are the same for each sheet in the workbook. Analyte
is different for each sheet.
- File Name - Imported
- Analyte - The analyte name is also the name of the worksheet (the tab label).
- Acquisition Date - Imported
- Reader Serial Number - Imported
- Standard Lot - Ignored in the header. The standard name also appears in the description for wells that contain the standard. The name of the standard for each analyte can be entered during the import process for each run.
- Expiration Date - Ignored
- Plate ID - Imported
- Signed By - Ignored
- Document ID - Ignored
- RP1 PMT (Volts) - Imported
- RP1 Target - Imported
Well data table
The data table in the middle of each sheet shows how each sample in each well reacted with the single analyte reported on the sheet. In other words, every well (and every sample) appears on every sheet, but each sheet reports on the behavior of a different analyte within that well.
File format variants
Samples (particularly unknowns) are typically replicated on a plate, in which case they will appear in multiple wells. How these replicates appear in the Excel file depends on the file format. LabKey Server understands three types of file formats.
- Variant A - Summary Data:
- The data table contains one row per sample. This row provides a calculated average of observed values for all sample replicates (all wells where the sample was run).
- The Wells column lists all the wells used to calculate the average.
- Variant B - Raw Data:
- The data table contains one row per well. That means that each sample replicate appears on its own line and the data reported for it is not averaged across sample replicates. Consequently, there are multiple rows for each experimental sample.
- Here, the Wells column shows only a single well.
- LabKey Server infers the presence of Variant B format if a files shows multiple rows for the same sample (so replicates are on different lines). Usually, all samples have the same number of replicates.
- Variant C - Summary and Raw Data:
- Two data tables appear, one following Variant A formatting and the second following Variant B. In other words, tables for both summary sample data and for individual well data both appear.
The data used in the tutorial follows the Variant B format. Two replicates were run for each unknown sample, so each unknown sample appears on two lines, one for each well where it was run.
The columns in the well data table:
- The analyte name is also the name of the worksheet (the tab label). In the data used in this tutorial, the analyte name is a combination of the analyte name and the number of the bead bound to the analyte.
- The letter portion of the "Type" indicates the kind of sample; the number portion (if there is one) provides a sample identifier
- B - Background. The average background fluorescence observed in a run's background wells is subtracted from each of the other wells to give the “FI - Bkgd” column
- S - Standard. The titration curve for the standard is used to calculate the concentration of unknowns
- C - Quality control. Used to compare with other runs and track performance
- X - Unknown. These are the experimental samples being studied.
- The plate location of the well where the sample was run. For file format Variant A, multiple wells may be listed here - these are all the wells for the sample replicate that have been averaged together to produce the average fluorescence intensity for the sample, as reported in FI
- For an unknown, identifies the source of the unknown sample. This may be a sample identifier or a combination of participant ID and visit number. The following formats are supported, and checked for in this sequence:
- <SpecimenID> - The value is checked for a matching specimen by its unique ID in the target study. If found, the specimen's participant ID and visit/date information is stored in the relevant fields in the Luminex assay data.
- <SpecimenID>: <Any other text> - Any text before a colon is checked for a matching specimen in the target study. If found, the specimen's participant ID and visit/date information is stored in the relevant fields in the Luminex assay data.
- <SpecimenID>; <Any other text> - Any text before a semi-colon is checked for a matching specimen in the target study. If found, the specimen's participant ID and visit/date information is stored in the relevant fields in the Luminex assay data.
- <ParticipantId>, Visit <VisitNumber>, <Date>, <ExtraInfo> - The value is split into separate fields. The "Visit" prefix is optional, as is the ExtraInfo value. The VisitNumber and Date values will be ignored if they cannot be parsed as a number and date, respectively.
- For file format Variant B, this is the median fluorescence intensity observed for all beads associated with this analyte type in this well.
- For file format Variant A, this value is the mean median fluorescence intensity for all sample replicate wells; in other words, it is a mean of all median FI values for the wells listed in the Wells column.
- Fluorescence intensity of well minus fluorescence intensity of a "background" (B) well
- Std Dev
- Standard of deviation calculated for replicate wells for file format Variant A
- Coefficient of variation calculated for replicate wells for file format Variant A
- Obs Conc
- Observed concentration of the titrated standard, quality control or unknown calculated by the instrument software. Calculated from the observed FI-Bkgd using the 5-parameter logistic regression that is reported at the bottom of the page as Std. Curve.
- Indicators: *Value = Value extrapolated beyond standard range; OOR = Out of Range; OOR> = Out of Range Above; OOR< = Out of Range Below
- Values of Obs Conc flagged as *Value and OOR receive substitutions (to more clearly show ranges) during import to LabKey Server. See: Luminex Conversions
- Exp Conc
- Expected concentration of the titrated standard or quality control. Known from the dilutions performed by the experiment performer. The Std. Curve equation listed at the bottom of the page reports the 5 parameter logistic regression equation that the instrument software fit to the distribution of the titration's FI-Bkgd and Exp Conc. The FitProb and ResVar for this regression are also listed.
- 100 times the ratio of observed and expected concentrations for titrated standard or quality control
- Indicators: *** = Value not available; --- = Designated as an outlier
- Not used in this tutorial
- Not used in this tutorial
- Dilution of the sample written as an integer. The actual dilution is a ratio, so a dilution of 1:100 is noted as 100
- Bead Count
- Sampling Errors
- Flags indicate sample errors
- Indicators: 1 - Low bead #; 2 - Agg beads; 3 - Classify %; 4 - Region selection; 5 - Platform temperature