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Chip type: HuGene-1_0-st-v1

Human Gene 1.0 ST Array

Affymetrix writes: "The GeneChip Human Gene 1.0 ST Array is the latest product in the family of Affymetrix expression arrays offering whole-transcript coverage. Each of the 28,869 genes is represented on the array by approximately 26 probes spread across the full length of the gene, providing a more complete and more accurate picture of gene expression than 3' based expression array designs. [...] The Gene 1.0 ST Array uses a subset of probes from the Human Exon 1.0 ST Array and covers only well-annotated content. Like the Exon 1.0 ST Array, "gene-level" analysis of multiple probes on different exons is summarized into an expression value representing all transcripts from the same gene."

HuGene-1_0-st-v1.r3

Note, the CDF downloaded from the Affymetrix website is in an ASCII (text) file format. It is highly recommended to work with binary CDFs instead since they are orders of magnitude faster to query and more memory efficient to work with. Use convertCdf() in the affxparser package to convert an ASCII CDF into binary.

> cdf <- AffymetrixCdfFile$byChipType("HuGene-1_0-st-v1",
tags="r3")
> cdf
AffymetrixCdfFile:
Path: annotationData/chipTypes/HuGene-1_0-st-v1
Filename: HuGene-1_0-st-v1,r3.cdf
Filesize: 16.67MB
Chip type: HuGene-1_0-st-v1,r3
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 1050x1050
Number of cells: 1102500
Number of units: 33252
Cells per unit: 33.16
Number of QC units: 0

HuGene-1_0-st-v1,Ensembl,exon

> cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Ensembl,exon")
> cdf
AffymetrixCdfFile:
Path: annotationData/chipTypes/HuGene-1_0-st-v1
Filename: HuGene-1_0-st-v1,Ensembl,exon.cdf
Filesize: 28.51MB
Chip type: HuGene-1_0-st-v1,Ensembl,exon
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 1050x1050
Number of cells: 1102500
Number of units: 27901
Cells per unit: 39.51
Number of QC units: 0

Resources

By aroma-project.org:

By Affymetrix: