GEAP

Gene Expression Analysis Platform

Type Checker Files


Illumina


Name
Extensions
Description
Priority
Data type
Download
Last Update
Illumina Non-Normalized
TXT

Non-normalized output data generated by Illumina platforms.

These files are available in GEO as supplementary files, and can be identified by a name like GSEXXXX_non-normalized.txt or similarly.

This file type contains a data table of probe intensity values and p-values, which is recognized by the pattern below:

ID_REF
Sample 1
Detection Pval
Sample 2
Detection Pval
...
ILMN_001
123.456
0.0123
234.567
0.0456
...
ILMN_002
987.654
0.0321
765.432
0.6540
...
ILMN_003
789.654
0.0132
567.234
0.0465
...
12
Series
01/26/2020


NanoString


Name
Extensions
Description
Priority
Data type
Download
Last Update
NanoString Markup RCC
RCC

RCC sample files available in GEO as supplementary files.

This file type has a markup syntax similar to HTML, whose elements contain the headers and the data table of detection intensities and probe identifiers.

					<Header>
					FileVersion,1.6
					SoftwareVersion,2.1.2.3
					</Header>
					...
					<Code_Summary>
					CodeClass,Name,Accession,Count
					Endogenous,GENE1,NM_0001,8
					Endogenous,GENE2,NM_0002,5
					...
					Endogenous,GENE9999,NM_9999,2
					</Code_Summary>
1
Sample
09/09/2020


NimbleGen


Name
Extensions
Description
Priority
Data type
Download
Last Update
NimbleScan Pair
PAIR

NimbleGen sample files available in GEO as supplementary files.

This file type contains a data table of probe intensity values, sequence identifiers and other annotations associated to each probe.

The last two columns represent values of probe perfect-match and mismatch. An option to remove probe mismatches during pre-analysis is available.

Sequence identifiers may be repeated, and an option to compute average expression values from duplicates is available.

# software=NimbleScan version=2.0.00 imagefile=...
IMAGE_ID
GENE_EXPR_OPTION
SEQ_ID
...
PM
MM
396138 CAPA 20100227A03__532
BLOCK1
AB00001
...
234.567
0.00
396138 CAPA 20100227A03__532
BLOCK1
AB00002
...
765.432
1.00
396138 CAPA 20100227A03__532
BLOCK1
AB00003
...
567.234
0.00
1
Sample
01/25/2020


What is a "Type Checker File"?


Type checker files are files created in GEAP Type Checker (TypeChecker.exe). They contain instructions to be executed during pre-analysis in order to identify, validate and process a specific file format.

There are two types of Type Checker Files: editable and compiled.

Editable files (.tcxml) are available to be edited or compiled through Type Checker.

Compiled files (.gtcheck) are loaded by GEAP and executed when an input file's extension matches one of the extensions from Type Checker file.
When the input file is validated and selected by the user, a dialog box with treatment options is displayed. If there is no option, this last step is ignored.

To install a compiled file, copy the .gtcheck file and paste inside .../GEAP/User/typecheck/ directory. GEAP will read the file on startup.
Type Checker Files with duplicated IDs are ignored.

Hint: Type Checker can be executed inside GEAP through Tools → File Format Checker. This method allows users to test and compile directly into GEAP.


Important note: Processing samples or annotations includes loading data into R environment, which requires knowledge of R programming.
Our team is developing a workaround concerning the programming step to facilitate the use of Type Checker by non-programmers.