Illumina BeadChip

Both BeadChip expression data files from Illumina's BeadStudio software and the corresponding BeadChip annotation files are supported by CLC Genomics Workbench. The formats of the BeadStudio and annotation files have changed somewhat over time and various formats are supported.

Illumina expression data, compact format

An example of this format is shown below: 

TargetID           AVG_Signal         BEAD_STDEV        Detection
GI_10047089-S      112.5              4.2               0.16903226
GI_10047091-S      127.6              4.8               0.76774194
All this information is imported into the Workbench. The AVG_Signal is used as the expression measure.

Download a small sample file here:
https://resources.qiagenbioinformatics.com/madata/IlluminaBeadChipCompact.txt

Illumina expression data, extended format

An example of this format is shown below: 

TargetID        MIN_Signal  AVG_Signal  MAX_Signal  NARRAYS  ARRAY_STDEV  BEAD_STDEV  Avg_NBEADS  Detection
GI_10047089-S   73.7        73.7        73.7        1        NaN          3.4         53          0.05669084
GI_10047091-S   312.7       312.7       312.7       1        NaN          11.1        50          0.99604483
All this information is imported into the Workbench. The AVG_Signal is used as the expression measure.

Download a small sample file here:
https://resources.qiagenbioinformatics.com/madata/IlluminaBeadChipExtended.txt

Illumina expression data, with annotations

An example of this format is shown below: 

TargetID	Accession	Symbol	Definition	Synonym	Signal-BG02 DCp32	 Detection-BG02 DCp32
GI_10047089-S	NM_014332.1	SMPX	"Homo sapiens small muscle protein, X-linked (SMPX), mRNA."		 -17.6	 0.03559657
GI_10047091-S	NM_013259.1	NP25	"Homo sapiens neuronal protein (NP25), mRNA."	NP22	 32.6	 0.99604483
GI_10047093-S	NM_016299.1	HSP70-4	"Homo sapiens likely ortholog of mouse heat shock protein, 70 kDa 4 (HSP70-4), mRNA."		 228.1	1
Only the TargetID, Signal and Detection columns will be imported, the remaining columns will be ignored. This means that the annotations are not imported. The Signal is used as the expression measure.

Download a small example sample file here:
https://resources.qiagenbioinformatics.com/madata/IlluminaBeadStudioWithAnnotations.txt

Illumina expression data, multiple samples in one file

This file format has too much information to show it inline in the text. You can download a small example sample file here:
https://resources.qiagenbioinformatics.com/madata/IlluminaBeadStudioMultipleSamples.txt

This file contains data for 18 samples. Each sample has an expression value (the value in the AVG_Signal column), a detection p-value, a bead standard deviation and an average bead number column. The workbench recognizes the 18 samples and their columns.

Illumina annotation files

The Workbench supports import of two types of Illumina BeadChip annotation files. These are either comma-separated or tab-delimited .txt files. They can be used to annotate experiments as shown in Adding annotations.

This file format has too much information to show it inline in the text.

Download a small example annotation file of the first type here:
https://resources.qiagenbioinformatics.com/madata/IlluminaBeadChipAnnotation.txt