HsEx10stv2_Hs_REFSEQ
Author: Mark Robinson
Created on: 2008-07-28
Human Exon Array -- "Brainarray" annotation
> cdf <- AffymetrixCdfFile$byChipType("HsEx10stv2_Hs_REFSEQ")
> cdf
AffymetrixCdfFile:
Path: annotationData/chipTypes/HsEx10stv2_Hs_REFSEQ
Filename: HsEx10stv2_Hs_REFSEQ.cdf
Filesize: 32.16MB
File format: v4 (binary; XDA)
Chip type: HsEx10stv2_Hs_REFSEQ
Dimension: 2560x2560
Number of cells: 6553600
Number of units: 56283
Cells per unit: 116.44
Number of QC units: 0
RAM: 0.00MB
> getUnitNames(cdf)[20789]
[1] "4136241_at"
> getUnitNames(cdf)[20790]
[1] "NM_000014_at"
Notes:
- The group from Michigan known as "Brainarray" (http://brainarray.mbni.med.umich.edu/) have created a number of "Custom CDF" files for a range of Affymetrix platforms.
- Above is an example of the REFSEQ probe organization for the Human Exon platform. Many other platforms are available for many organisms.
- Note that with the 56,283 units for this chip, the first 20,789 are not RefSeqs. I think they are genomic background probes, but I'm not sure.
- To download one of these for your favourite chip, click on the "Download Custom CDF Files" link from http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp
- The file you will want is the <chip_organism_mapping>.cdf which is
contained in the zip file under the column "CDF&Seq&Map&Desc". It
is an ASCII cdf file, so be sure to use
convertCdf()
to convert it to binary before using it for processing data.
CAUTION:
If you have overlapping transcripts (which RefSeq
almost surely will have), then be VERY careful if you are using the
stored probe affinities. Because with overlapping transcripts, you
have probes that belong to multiple probesets and they will have
possibly different estimate probe effects in the different
probesets, when these get written to the 'probeAffinities.cel' file,
the indices will clash and only one probe effect will be stored.
The chip effects (i.e. gene-level expression summaries) are
unaffected by this, so if you do not need to manually access the
probe affinities, there is no worry.