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Chip type: HuEx-1_0-st-v2

GeneChip Human Exon 1.0 ST Array 

Affymetrix press release: Affymetrix Launches GeneChip(R) Human Exon Array - New Microarray Offers Exon-Level, Genome-Wide Expression Profiling on a Single Array, Oct 3, 2005.

Comments: ST == Sense Target.
 

HuEx-1_0-st-v2

Affymetrix offers a by them unsupported CDF for the chip type HuEx-1_0-st-v2.

> cdf <- AffymetrixCdfFile$byChipType("HuEx-1_0-st-v2")
> print(cdf)
AffymetrixCdfFile:
Path: annotationData/chipTypes/HuEx-1_0-st-v2/ASCII
Filename: HuEx-1_0-st-v2.cdf
Filesize: 933.84MB
File format: v3 (text; ASCII)
Chip type: HuEx-1_0-st-v2
Dimension: 2560x2560
Number of cells: 6553600
Number of units: 1432154
Cells per unit: 4.58
Number of QC units: 0RAM: 0.00MB

This is a CDF per exon: each unit has one group/probeset, which is the exon. There is no information about clustering exons/probesets into genes -- see the following subpages for options for CDFs with clusterings of exons into gene models. There are also a number of strange probesets corresponding to control probes which can contain VERY large numbers of probes per probeset and significantly slow down RMA fitting.  See Thread 'Ram option is aroma Options' (Nov 8, 2007), for examples. These probesets should be removed or one of the CDFs below which do not contain them should be used.

Note I: 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 magnitute faster to query and more memory efficient to work with.  Use convertCdf() in the affxparser package to convert an ASCII CDF into binary.

Note II: Older CEL files for this chip type, may be reported to have chip type 'HuEx-1_0-st-v1'.  This chip is slightly different from the 'HuEx-1_0-st-v2' chip.  According to Affymetrix support, the difference is only in the control probes; "There is only a minor difference between the v1 and the v2 library files and it has to do with the manufacturing controls on the array. There is no difference with the probes interrogating the exons between v1 and v2.", cf. Thread 'Discussion on affymetrix-defined-transcript-clusters' (Nov 25-Dec 2, 2008).  We don't have details on the exact differences and we don't have access to the HuEx-1_0-st.v1.CDF (please fwd if you have it), but from Affymetrix' feedback it sounds like one could use the new HuEx-1_0-st-v2.CDF.  In aroma.affymetrix, one can override the default CDF by:

cdf <- AffymetrixCdfFile$byChipType("HuEx-1_0-st-v2");
csR <- AffymetrixCelSet$byName("MyDataSet", cdf=cdf);

Resources

By aroma-project.org:

The following subpages contain custom CDFs that map the exon array probes to gene models:

  • Affymetrix-Defined transcript clusters are a 'gene model' of sorts defined by clustering of exons automatically done by Affymetrix. The CDF contains both the transcript clusters as well as the exon identifications of the probes in a nested fashion.
  • Ensembl Gene Defintions gene models based on the Ensembl annotation.
  • HsEx10stv2_Hs_REFSEQ give some notes regarding regarding custom CDFs from U Michigan that map the exons to RefSeq transcript identifications.

If you would like to contribute a custom-made CDF that would be great. Please give your file descriptive tags that indicate either the date of creation or the date of the annotation on which it is based (something like: HuEx-1_0-st-v2,MyFavAnnot,20070525,xx.cdf where xx are you or your institution's initials) and create a page describing how it was made. Please do not give it a name of a pre-existing CDF available here! Contact Elizabeth Purdom (epur...@stat.berkeley.edu) if you need assistance with contributing a CDF.

 

By Affymetrix: