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Selecting a Template for Data Import

 

Overview

 

GeneLinker™ can read expression data files produced by a wide variety of other software. GeneLinker™ uses a template to interpret the contents of your data file or files.

 

Data files containing one sample each:

Template Name

Template Description

Affymetrix 4.0

Import Affymetrix MAS 4.0 data files.

Affymetrix 5.0

Import Affymetrix MAS 5.0 data files.

CodeLink

Import CodeLink XML files.

dChip paired xls files

Import dChip paired xls files.

GenePix

Import GenePix ATF data files.

Koadarray

Import single channel or two color Koadarray files.

GenePix Green/Red

Import GenePix ATF two-color data values (treatment=green/control=red).

GenePix Merge Replicates

Import GenePix ATF data files and generate reliability measures by merging replicates (see Merging Within-Chip Replicate Measurements).

GenePix Red/Green

Import GenePix ATF two-color data values (treatment=red/control=green).

Genomic Solutions

Import Genomic Solutions files.

Genomic Solutions Merge Replicates

Import Genomic Solutions data files and generate reliability measures by merging replicates (see Merging Within-Chip Replicate Measurements).

Quantarray

Import Quantarray data values into a two-color dataset.

ScanArray

Import ScanArray data files.

ScanArray Merge Replicates

Import ScanArray data files and generate reliability measures by merging replicates (see Merging Within-Chip Replicate Measurements).

ScanArray TwoColor (Ch1/Ch2)

Import ScanArray two-color data values (treatment=Ch1/control=Ch2).

ScanArray TwoColor (Ch2/Ch1)

Import ScanArray two-color data values (treatment=Ch2/control=Ch1).

Spectral (proteomics) Data

Import spectral (proteomics) data and peak files.

 

Data files containing all samples in one file:

Multi-Sample Data File

Template Description

DCHIP single xls file

Import dChip single xls data file.

Tabular

Import tabular data from a single multi-sample data file.

Tabular Merge Replicate Columns

Import tabular data with genes represented by columns and generate reliability measures by merging replicate genes (see Merging Within-Chip Replicate Measurements). Be sure this is what you want. Tabular files more typically have genes in rows!

Tabular Merge Replicate Rows

Import tabular data with genes represented by rows and generate reliability measure by merging replicate genes (see Merging Within-Chip Replicate Measurements).

Tabular with Reliability Measures

If you have generated reliability measures for tabular data independently of GeneLinker™, it is possible to import them along with your data. They must be in a tabular file of identical shape to your gene expression data file. If your gene expression data file is named FileName.ext then your reliability measures must be in a file named FileName_rm.ext in the same folder. GeneLinker™ expects that reliability measures will be between 0 and 1 inclusive, and that values close to 0 will indicate highly reliable data.

 

If you do not see a format in the lists above that matches the format of your data, your best course of action is to transform your data into Tabular format. See Importing Data from Tabular Files for more information.

 

Actions

1. Click the Import Gene Expression Data toolbar icon , or select Import from the File menu and Gene Expression Data from the sub menu. The Data Import dialog is displayed.

2. Select a Gene Database from the drop-down list. This tells GeneLinker™ which type of gene identifier the genes being imported have (GenBank, Affymetrix, UniGene, or custom). If you need more information about this, see Selecting the Gene Database Type. You can also select the gene database after you have changed templates if you wish.

 

The name of the selected template appears on the Data Import dialog. If this is the appropriate template for your data, go to either Importing One File Containing All Samples, or Importing Multiple Files With One Sample Each, as appropriate to the template you have selected.

If the appropriate template name is not showing on the dialog, then continue:

 

3. Click the template that is appropriate for your data file(s) from the drop-down list. The template is highlighted.

4. To set the selected template as the default, click the Set As Default button. If you will be importing data of the same format repeatedly, you should do this so you will not need to re-select the same template each time you import data. When this button is inactive (text is grey) the displayed template is the default template.

5. Click Select.

Go to Importing One File Containing All Samples.

 

Go to Importing Multiple Files With One Sample Each.

 

Note: gene identifiers have a length restriction of 25 characters. This means that on import of a dataset or a gene list, identifiers that are longer than 25 characters are truncated.

 

Related Topics:

Importing One File Containing All Samples

Importing Multiple Files With One Sample Each

Merging Within-Chip Replicate Measurements