## Supported chip types

Currently the following chip types have annotation packages in Chipster, which means that they can be annotated and used for pathway and promoter analysis. Please note that if your array doesn't appear on the list, you can still bring the data into Chipster and run preprocessing, statistical analysis and clustering for it. The only exception is Affymetrix data, which requires the CDF and probe packages for the preprocessing to work. Currently some Affymetrix chip types (marked with asterisk on the list) have only the CDF and probe packages in Chipster, which means that the annotation based analyses are not available for them. The names in brackets indicate the annotation package names, which you need to use (with the ending .db) to define the chiptype if bringing normalized data into Chipster.

### Affymetrix - 3' expression

- Arabidopsis Genome Array (ag)
- Arabidopsis ATH1 Genome Array (ath1121501)
- C. elegans Genome Array (celegans)
- Barley Genome *
- Bovine Genome (bovine)
- Canine Genome (canine)
- Canine Genome 2.0 (canine2)
- Chicken Genome (chicken)
- Citrus Genome *
- Drosophila Genome Array (drosgenome1)
- Drosophila Genome 2.0 Array (drosophila2)
- Human Genome U133 Set, HG-U133A (hgu133a)
- Human Genome U133A 2.0 Array (hgu133a2)
- Human Genome U133 Plus 2.0 Array (hgu133plus2)
- Human Genome U95 Set, HG-U95A (hgu95a)
- Human Genome U95 Set, HG-U95Av2 (hgu95av2)
- Maize Genome *
- Medicago Genome *
- Murine Genome U74v2, MG-U74A (mgu74a)
- Murine Genome U74v2, MG-U74Av2 (mgu74av2)
- Murine Genome U74v2, MG-U74Bv2 (mgu74bv2)
- Murine Genome U74v2, MG-U74Cv2 (mgu74cv2)
- Mouse Expression Set 430 (moe430a)
- Mouse Genome 430 2.0 Array (mouse4302)
- Mouse Genome 430A 2.0 Array (mouse430a2)
- Plasmodium / Anopheles Genome *
- Poplar Genome *
- Porcine Genome *
- Pseudomonas aeruginosa (paeg1a)
- Rat Expression Set 230 (rae230a)
- Rat Genome 230 2.0 Array (rat2302)
- Rat Genome U34 Set (rgu34a)
- Rhesus Macaque Genome *
- Rice Genome *
- Soybean Genome *
- Sugar Cane Genome *
- Tomato Genome *
- Vitis Vinifera Genome *
- Wheat Genome *
- Yeast Genome 2.0 Array (yeast2)
- Yeast Genome S98 Array (ygs98)
- Xenopus laevis Genome Array *
- Zebrafish Genome Array (zebrafish)

### Affymetrix - Exon arrays

- Human 1.0 ST (huex10stv2hsentrezg)
- Mouse 1.0 ST (moex10stv1mmentrezg)
- Rat 1.0 ST (raex10stv1rnentrezg)

### Affymetrix - Gene arrays

- Human 1.0 ST (hugene10stv1hsentrezg)
- Mouse 1.0 ST (mogene10stv1mmentrezg)
- Rat 1.0 ST (ragene10stv1rnentrezg)

### Affymetrix - SNP arrays

- Genome-Wide Human SNP Array 6.0 (pd.genomewidesnp.6)
- Genome-Wide Human SNP Array 5.0 (pd.genomewidesnp.5)
- Human Mapping 500K Array Set

- Human Mapping 250K Nsp Array (pd.mapping250k.nsp)
- Human Mapping 250K Sty Array (pd.mapping250k.sty)

- Human Mapping 100K Set

- Human Mapping 50K Array Xba 240 (pd.mapping50k.xba240)
- Human Mapping 50K Array Hind 240 (pd.mapping50k.hind240)

### Illumina

- Sentrix Human-6 v1 (illuminaHumanv1)
- Sentrix HumanRef-8 v1 (illuminaHumanv1)
- Sentrix Human-6 v2 (illuminaHumanv2)
- Sentrix HumanRef-8 v2 (illuminaHumanv2)
- Sentrix Human-6 v3 (illuminaHumanv3)
- Sentrix HumanRef-8 v3 (illuminaHumanV3)
- Sentrix Human HT-12 (IlluminaHumanv4)
- Sentrix Mouse-6 v1.0a (illuminaMousev1)
- Sentrix MouseRef-8 v1.0a (illuminaMousev1)
- Sentrix Mouse-6 v1.1 (illuminaMousev1p1)
- Sentrix MouseRef-8 v1.1 (illuminaMousev1p1)
- Sentrix Mouse-6 v2 (illuminaMousev2)
- Sentrix MouseRef-8 v2 (illuminaMousev2)
- Sentrix RatRef-12 v1 (illuminaRatv1)

### Agilent

- Human 1 (hgug4100a)
- Human 2 (hgug4101a)
- Human 1A (V2) (hgug4110b)
- Human 1B (hgug4111a)
- Human Genome, Whole (hgug4112a)
- Mouse (mgug4104a)
- Mouse (mgug4120a)
- Mouse Genome (mgug4121a)
- Mouse Genome, Whole (mgug4122a)
- Rat (rgug4105a)
- Rat (rgug4130a)

### Agilent aCGH arrays

Chipster offers a tool for fetching probe coordinates from the CanGEM database.

- Human Genome CGH Oligo Microarray 4x44K
- Human Genome CGH Oligo Microarray Kit 244A, "G4411B"
- Human Genome CGH Oligo Microarray Kit 44A, "G4410A"
- Human Genome CGH Oligo Microarray Kit 44B, "G4410B"

### Agilent miRNA arrays

- Human-miRNA v1 (miRNA)
- Human-miRNA v2 (miRNA)
- Human-miRNA v3 (miRNA)
- Mouse-miRNA v1 (miRNA)
- Mouse-miRNA v2 (miRNA)
- Rat-miRNA (miRNA)

### Exiqon

- Arrays with miRNA systematic names, like hsa-miR-31 (miRNA)