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."
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$byChipType("HuGene-1_0-st-v1", tags="r3") > cdf AffymetrixCdfFile: Path: annotationData/chipTypes/HuGene-1_0-st-v1 Filename: HuGene-1_0-st-v1,r3.cdf Filesize: 16.67MB Chip type: HuGene-1_0-st-v1,r3 RAM: 0.00MB File format: v4 (binary; XDA) Dimension: 1050x1050 Number of cells: 1102500 Number of units: 33252 Cells per unit: 33.16 Number of QC units: 0
> cdf <- AffymetrixCdfFile$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
- The binary version of the Affymetrix unsupported CDF. Created by Mark Robinson on 2008-08-28.
- HuGene-1_0-st-v1,Ensembl,exon.cdf.gz - The Ensembl-centric (gene and exon) CDF used in the FIRMAGene paper (Robinson & Speed, 2007). This file is identical to HuGene_Ensembl_EXON.cdf linked to in that paper. Created by Mark Robinson in 2007.
- Product page: Human Gene 1.0 ST Array