• Sign In

Search site

HIV Study Tutorial
Found 314 results
Displaying page 2 of 16

ImmuneScore - Assay.xlsx

data ParticipantID Date VisitId SpecimenId M1 M2 M3 InstrumentSetting OperatorEmail Comment PT-101 1/1/08 1 vl-100 28.0 31.0 90.5 3.0 john@labkey.com PT-101 2/2/08 2 vl-100 29.0 42.0 87.0 4.0 john@labkey.com PT-101 3/3/08 3 vl-100 13.5 66.0 90.0 2.0 john@labkey.com PT-101 4/4/08 4 vl-100 13.0 53.5 89.0 4.0 john@labkey.com PT-101 5/5/08 5 vl-100 35.5 69.0 80.0 2.0 john@labkey.com PT-101 6/6...

"ViralLoadPCR.xls" attached to page "Tutorial: Inferring Datasets from Excel and TSV Files"

data ParticipantId VisitId Date ViralLoad_PCR PT-101 9 2020-10-11 622266 PT-101 10 2020-11-08 516034 PT-101 11 2020-12-06 754050 PT-101 12 2021-01-03 612305 PT-101 13 2021-01-31 553552 PT-101 14 2021-02-28 873787 PT-101 15 2021-03-28 572848 PT-101 16 2021-04-25 631916 PT-101 17 2021-05-23 478317 PT-101 18 2021-06-20 464987 PT-101 19 2021-07-18 290176 PT-101 20 2021-08-15 269040 PT-101...

"ViralLoadNASBA.xls" attached to page "Tutorial: Inferring Datasets from Excel and TSV Files"

data ParticipantId VisitId Date ViralLoad_NASBA PT-101 18 2021-06-20 543353 PT-101 3 2020-04-26 1826358 PT-101 4 2020-05-24 188663 PT-101 5 2020-06-21 209751 PT-101 6 2020-07-19 229473 PT-101 24 2021-12-05 185269 PT-101 23 2021-11-07 232166 PT-101 7 2020-08-16 254867 PT-101 8 2020-09-13 290320 PT-101 9 2020-10-11 492442 PT-101 22 2021-10-10 178996 PT-101 21 2021-09-12 200846 PT-101 20...

"ViralLoadPCR.xls" attached to page "Step 2: Import Datasets"

data ParticipantId SequenceNum Date ViralLoad_PCR PT-101 9 2020-10-11 622266 PT-101 10 2020-11-08 516034 PT-101 11 2020-12-06 754050 PT-101 12 2021-01-03 612305 PT-101 13 2021-01-31 553552 PT-101 14 2021-02-28 873787 PT-101 15 2021-03-28 572848 PT-101 16 2021-04-25 631916 PT-101 17 2021-05-23 478317 PT-101 18 2021-06-20 464987 PT-101 19 2021-07-18 290176 PT-101 20 2021-08-15 269040 PT-101...

"ViralLoadPCR.xls" attached to message "Date error msg: "couldn’t convert date field, should be of type timestamp""

data ParticipantId SequenceNum Date ViralLoad_PCR PT-101 9 10/11/20 622266 PT-101 10 11/8/20 516034 PT-101 11 12/6/20 754050 PT-101 12 1/3/21 612305 PT-101 13 1/31/21 553552 PT-101 14 2/28/21 873787 PT-101 15 3/28/21 572848 PT-101 16 4/25/21 631916 PT-101 17 5/23/21 478317 PT-101 18 6/20/21 464987 PT-101 19 7/18/21 290176 PT-101 20 8/15/21 269040 PT-101 21 9/12/21 213870 PT-101 22 10...

"PhysicalExam.xls" attached to page "Tutorial: Inferring Datasets from Excel and TSV Files"

data ParticipantId VisitId Date Weight_lb Temperature_F SystolicBloodPressure DiastolicBloodPressure Pulse Clinician_Signature_Date PT-101 23 2021-11-07 145 99.4 122 91 68 FALSE PT-101 24 2021-12-05 148 97.2 113 90 65 FALSE PT-101 22 2021-10-10 197 97.9 109 95 72 FALSE PT-101 21 2021-09-12 146 94.4 124 86 64 FALSE PT-101 20 2021-08-15 187 98.7 128 88 80 FALSE PT-101 19 2021-07-18 170 101.1...

"PhysicalExam.xls" attached to page "Step 2: Import Datasets"

data ParticipantId SequenceNum Date Weight_lb Temperature_F SystolicBloodPressure DiastolicBloodPressure Pulse Clinician_Signature_Date PT-101 23 2021-11-07 145 99.4 122 91 68 FALSE PT-101 24 2021-12-05 148 97.2 113 90 65 FALSE PT-101 22 2021-10-10 197 97.9 109 95 72 FALSE PT-101 21 2021-09-12 146 94.4 124 86 64 FALSE PT-101 20 2021-08-15 187 98.7 128 88 80 FALSE PT-101 19 2021-07-18 170 101.1...

Hematology.xlsx

data ParticipantID SequenceNum VisitName SpecimenId Date CD4 Lymphocytes Hemoglobin Comment PT-101 1 Visit 1 vl-100 1/1/08 860 1527 14 CD4 PT-101 2 Visit 2 vl-100 2/2/08 825 1689 15 700 PT-101 3 Visit 3 vl-100 3/3/08 851 1601 14 900 PT-101 4 Visit 4 vl-100 4/4/08 767 1762 14 PT-101 5 Visit 5 vl-100 5/5/08 774 1386 12 Lymphocytes PT-101 6 Visit 6 vl-100 6/6/08 800 1467 17 1200 PT-101 7 Visit...

"LabResults.xls" attached to page "Tutorial: Inferring Datasets from Excel and TSV Files"

data ParticipantId VisitId Date CD4 Lymphocytes Hemoglobin PT-101 18 2021-06-20 843 2374 13.0 PT-101 3 2020-04-26 210 553 11.0 PT-101 4 2020-05-24 223 805 13.0 PT-101 5 2020-06-21 351 941 11.0 PT-101 6 2020-07-19 298 847 14.0 PT-101 24 2021-12-05 768 2060 11.0 PT-101 23 2021-11-07 744 2334 12.0 PT-101 7 2020-08-16 404 2549 12.0 PT-101 8 2020-09-13 536 1425 15.0 PT-101 9 2020-10-11 475 1654...

"LabResults.xls" attached to page "Step 2: Import Datasets"

data ParticipantId SequenceNum Date CD4 Lymphocytes Hemoglobin PT-101 18 2021-06-20 843 2374 13.0 PT-101 3 2020-04-26 210 553 11.0 PT-101 4 2020-05-24 223 805 13.0 PT-101 5 2020-06-21 351 941 11.0 PT-101 6 2020-07-19 298 847 14.0 PT-101 24 2021-12-05 768 2060 11.0 PT-101 23 2021-11-07 744 2334 12.0 PT-101 7 2020-08-16 404 2549 12.0 PT-101 8 2020-09-13 536 1425 15.0 PT-101 9 2020-10-11 475...

"testFile.csv" attached to message "Date error msg: "couldn’t convert date field, should be of type timestamp""

ParticipantId SequenceNum Date CD4 Lymphocytes Hemoglobin PT-101 18 2021-06-20 843 2374 13.0 PT-101 3 2020-04-26 210 553 11.0 PT-101 4 2020-05-24 223 805 13.0 PT-101 5 2020-06-21 351 941 11.0 PT-101 6 2020-07-19 298 847 14.0 PT-101 24 2021-12-05 768 2060 11.0 PT-101 23 2021-11-07 744 2334 12.0 PT-101 7 2020-08-16 404 2549 12.0 PT-101 8 2020-09-13 536 1425 15.0 PT-101 9 2020-10-11 475 1654...

"LabResults.xls" attached to message "Date error msg: "couldn’t convert date field, should be of type timestamp""

data ParticipantId VisitId Date CD4 Lymphocytes Hemoglobin PT-101 18 6/20/21 0:00 843 2374 13 PT-101 3 4/26/20 0:00 210 553 11 PT-101 4 5/24/20 0:00 223 805 13 PT-101 5 6/21/20 0:00 351 941 11 PT-101 6 7/19/20 0:00 298 847 14 PT-101 24 12/5/21 0:00 768 2060 11 PT-101 23 11/7/21 0:00 744 2334 12 PT-101 7 8/16/20 0:00 404 2549 12 PT-101 8 9/13/20 0:00 536 1425 15 PT-101 9 10/11/20 0:00 475...

Participant Aliases

A single study participant can be known by different names in different research contexts. One lab might refer to the subject using the name "LK002-234001", whereas another lab might use the name "Primate 44". It is often necessary (and even desirable) to let the different providers of data use their own names, rather than try to standardize them at the various sources. LabKey Server can align all...

Example Workflow: Develop a Transformation Script

This topic describes the process for developing a transformation script to transform assay data. You can use transformation scripts to change both run data and run properties as needed. In this example, we use perl, but using any scripting language will follow these general steps. Script Engine Setup Add Script to Assay Design Download Template Files Define the Desired Transformation Write...

Import Visit Names / Aliases

When data is collected by different sites and organizations, it can be difficult to keep visit naming standards consistent. The datasets generated might use many different ways of referring to the same visit. For example, the following list of values might all refer to the same visit: "Month 1" "M1" "Day 30" "First Month" Instead of editing your datasets to force them to be consistent, you...

dataset001.tsv

patient_document date participant_id study_id testfield2 testfield1 participantId meds given_birth eat first_name email specify_mood height aerobics address comments telephone_1 sex last_name weight drink date_enrolled dob gym age bmi Consent.docx Wed Jun 16 02:02:01 PDT 2021 PT-101 Malcolm Malcolm SpaceCowboy@gmail.com 53 187 Thursday,Tuesday 101 Serenity Ship, Out-of-sight, NoWhere, 18533...

"Demographics.xls" attached to page "Tutorial: Inferring Datasets from Excel and TSV Files"

Sheet1 ParticipantId VisitId Date StartDate Country PrimaryLanguage Sex TreatmentGroup StatusOfInfection PT-101 0 2020-02-02 2020-02-02 Germany German f ETR HIV Positive PT-102 0 2020-02-02 2020-02-02 USA English f DRV HIV Positive PT-103 0 2020-02-02 2020-02-02 USA English m No Treatment HIV Positive PT-104 0 2020-02-02 2020-02-02 USA French m HIV Negative HIV Negative PT-105 0 2020-02-02 2020-02-02...

"Demographics.xls" attached to page "Step 2: Import Datasets"

Sheet1 ParticipantId SequenceNum Date StartDate Country PrimaryLanguage Sex TreatmentGroup StatusOfInfection PT-101 0 2020-02-02 2020-02-02 Germany German f ETR HIV Positive PT-102 0 2020-02-02 2020-02-02 USA English f DRV HIV Positive PT-103 0 2020-02-02 2020-02-02 USA English m No Treatment HIV Positive PT-104 0 2020-02-02 2020-02-02 USA French m HIV Negative HIV Negative PT-105 0 2020-02-02...

JOIN Queries

This topic covers using JOIN in LabKey SQL to bring data together. All data is represented in tables, or queries. A list or dataset or user defined query are all examples of queries. Queries are always defined in a specific folder (container) and schema, but can access information from other queries, schema, and folders using JOINs. JOIN Columns from Different Tables Handle Query/Table Names...

Linking Data Records to Image Files

This topic explains how to link data grids to image files which reside either on the same LabKey Server, or somewhere else on the web. This feature can be used with any LabKey data table as an alternative to propertyFields. For assay designs, see the following topic: assayImage. Scenario biopsies5.png Suppose you have a dataset where each of row of data refers to some image or file. For example,...