# Presentation: 197977

## Using Cvt2Mae to Convert User-Defined Array Data for MAExplorer http://www.lecb.ncifcrf.gov/Cvt2Mae

- Peter F. Lemkin(1), Greg Thornwall (2), Bob Stephens(3)
- (1) LECB/NCI/FCRDC, (2) SAIC/FCRDC, (3) ABCC/FCRDC
- DRAFT - Revised: 01-28-2002
- Cvt2Mae version 0.60

## Accessing Arrays with MAExplorer

- MAExplorer works with any arrays using the schema (see Appendix C of MAExplorer Reference Manual for details)
- All data files are tab-delimited text files
- Databases could be constructed with tools like Excel for editing user data into the schema format
- The _Cvt2Mae array data converter_ “Wizard” tool converts non-standard **<User-defined>** academic or commercial data to MAExplorer format
- Affymetrix, Incyte, GenePix, Scanalyze, and other array data formats may be converted using predefined “Array Layouts”

## S.1 MAExplorer Data Schema

- MAExplorer works with any array data using our data schema
- The schema is described in detail in MAExplorer Reference Manual Appendix C._ _
- _Data Schema_: tab-delimited experiment data files:                                                                  1.  GIPO  (_G_ene _I_n _P_late _O_rder or “array print” file)                                                                                    2.  List of hybridized samples in database                                                                              3.  Configuration data describing the array and conventions                                                                                         4.  Separate spot quantification data files
- The _Cvt2Mae_ “wizard” tool converts user array data to this schema

## S.1.1 MAExplorer GIPO or Print File

- GIPO file maps a spot on the array to a particular gene
- Contains:
-      1. location or grid-geometry
-      2. one or more genomic identifiers (e.g., Clone ID, GenBank                                                                                                                                                                                                    ID, LocusID, or simply Location etc.)
-      3. gene description as Gene Name (or other description)
-      4. Optional: global spot quality (QualCheck)
-      5. optional: plate coordinates for clones

## S.1.2 MAExplorer Samples Database File

- List of hybridized samples file _SamplesDB.txt_ file contains:
-   1. full sample description
-   2. base file name of quantification file (without .quant file                                                                                                                                                                                                  extension)
-   3. optional sample ID number
-   4. other data you wish to carry with the samples (used in array                                                                                                                                                                                                reports)

## S.1.3 MAExplorer Configuration Database File

- Configuration data file _MaeConfig.txt_ describes particular type of array and hybridization labeling you are using. This includes:
- grid-geometry - # of replicate fields, grids, rows/grid, columns/grid
- spot hybridization labeling - intensity or ratio data, dye names
- various presentation options - use pseudo-array or actual (x,y) coordinates, etc.

## S.1.4 MAExplorer Spot Quantification Files

- Separate spot quantification data files (with _.quant_ file extension) are used for each hybridized sample
- 33P or biotin labeled samples are specified as one hybridization intensity information per file
- Fluorescent Cy3/Cy5-dye labeled samples are specified as two channels of hybridization intensity information per file
- Intensity background data is optional
- Spot quality (QualCheck) data is optional
- Grid-coordinates are specified the same as for GIPO file

## S.2 Assumptions About User Data - Array Layout

- User data is _tab-delimited ASCII text_ files (could generate with Excel)
- If the array geometry (#fields, grids, rows/grid, columns/grid) is known, that geometry may be used in MAExplorer
- Otherwise, a _pseudo-array_ geometry is generated for visual use in MAExplorer from the total # of spots in the user data
- An _Array Layout_ describes the user data. It may be edited and saved for subsequent use in converting other array data files of the same type
- The _<User-defined>_ array layout gives users complete flexibility in describing the array

## S.3 Example of tab-delimited GIPO Data

## S.3.1 Example of tab-delimited User-Defined Data

## I.  Procedure: Convert Data for Array Layouts

-     1. Select the Chip Set array layout if in list,  otherwise
-         pick **<User-defined>)**
-     2. Select separate GIPO file if needed using the “Browse GIPO file” .
-     2.1 Repeatedly select 1 or more input files using the “Browse input files”
-     3. You may edit or change various array layout parameters at this time
-        3.1 you may edit the array layout with “Edit Layout”
-        3.2 you may “Assign GIPO fields” in user data file
-        3.3 you may “Assign _Quant_ification fields” in user data file
-        3.4 if you changed any array layout parameters, you may save it with                                                                                                                                                                                            “Save Layout”

## I.  Procedure: continued...

-     4. Select the project output directory (i.e., folder) to save generated files
-     5. Press “Run” to convert the data
-     6. Press “Done” when it is finished.
-     7. Go to the project directory and then to the MAE sub-directory, click on the  _Start.mae_ file to start MAExplorer on the new data

## 1. Initial State of Cvt2Mae Program

## 2. Selecting <User-defined> Chipset Array-Layout

## 2.1 For this example, select “separate GIPO” and deselect “Mult. Samples/file”

## 3.1 Select GIPO Input File with “Browse GIPO file”

## 3.2 Specify GIPO Field Names for Grid, Row & Column

## 3.3 Select Files with “Browse input file” Name

## 4. Continue Adding Input Files If Needed

## 5.1 Edit Layout ‘Wizard’ Values for This Array

## 5.2 Edit Layout ‘Wizard’ - Grid Geometry. Deselect “Specify layout by #”

## 5.2.1 Edit Layout ‘Wizard’ - Grid Geometry. Enter (Grid, Rows/Grid, Columns/Grid) Values

## 5.3 Edit Layout ‘Wizard’ Input Data File Row Values. Verify Row Where Field Names Defined

## 5.3.1 Edit Layout ‘Wizard’ Input GIPO File Row Values. Verify Row Where Field Names Defined

## 5.4 Edit Layout ‘Wizard’ Ratio or Intensity Values. Select “background” and “Use Ratio”

## 5.5 Edit Layout ‘Wizard’ optional (X,Y) Coordinate Values for your data

## 5.6 Edit Layout ‘Wizard’ Genomic ID Values. Select “Clone ID”

## 5.7 Edit Layout ‘Wizard’ Gene Names Description. Selecting “QualCheck”

## 5.8 Edit Layout ‘Wizard’ Calibration Values. Define UniGene Species prefix

## 5.9 Edit Layout ‘Wizard’ Database Name Values. Define Optional Names for Database

## 5.10 Edit Layout ‘Wizard’ HP-X,-Y Class Names

## 5.11 Edit Layout ‘Wizard’ Default Thresholds

## 6. Other Options - Assigning User Data Fields to MAExplorer Fields

- _GIPO_ (Gene In Plate Order or “array print” table) - assigns genes to positions on the array as well as GeneBank ID, Clone ID, LocusID (if available), Gene Name, etc.
- _Quant data_ - assigns names of quantified data in the user file to MAExplorer data (e.g. Cy3 intensity to RawIntensity1, Cy5 to RawIntensity2, etc).

## 6.1 “Assign user fields to GIPO fields”

## 6.2 “Assign user fields to Quant fields”

## 7. Optional “Save Layout” to Array Layout Database After Edit Layout and Assign fields

## 8. Specifying “Create new project folder” Option Where Generated Database Will Be Saved

## 8.1 Specifying  New “Project Output Folder”

## 8.2 “Project Output Folder” & MAE startup file

## 9. Conversion in Process After Pressing “RUN”

## 10. Notification that Conversion is Finished

## 11. MAExplorer Data Created By Cvt2Mae

## 12. Running MAExplorer on the Converted Data