analysis of HuGene-1_1-st-v1

[dave]

Hi,

I hope I am not asking a too simple question but I am trying to load
affy HuGene-1_1-st-v1 chips on aroma.affymetrix. I have been away from
affy analysis for a while so maybe this is a known thing. I cannot
find the corresponding cdf file (in affymetrix webpage they seem to
have modified the files). I tried with the HuGene-1_0-st-v1 cdf file
(which seems to work for dChip analysis) renaming it but gave me an
error:

> cdf <- AffymetrixCdfFile$byChipType("HuGene-1_1-st-v1")
> cdf
AffymetrixCdfFile:
Path: annotationData/chipTypes/HuGene-1_1-st-v1
Filename: HuGene-1_1-st-v1.cdf
Filesize: 16.67MB
Chip type: HuGene-1_1-st-v1
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 1050x1050
Number of cells: 1102500
Number of units: 33252
Cells per unit: 33.16
Number of QC units: 0
> chipType <- "HuGene-1_1-st-v1"
> cs <- AffymetrixCelSet$byName("Samples", cdf=cdf)
Error en method(static, ...) :
[2012-06-11 17:15:28] Exception: Failed to setup a data set for any of
1 data directories located. The following reasons were reported: (1)
Cannot set CDF. The specified CDF structure ('HuGene-1_1-st-v1') is
not compatible with the chip type ('HuGene-1_1-st-v1') of the CEL
file. The number of cells do not match: 1102500 != 1178100 (while
trying 'rawData/Samples/HuGene-1_1-st-v1').

Can anyone help me?

Thanks

Dave


> sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: i386-pc-mingw32/i386 (32-bit)

attached base packages:
[1] stats graphics grDevices utils datasets methods
base

other attached packages:
[1] hugene11stv1hsentrezgcdf_15.1.0 AnnotationDbi_1.16.19
Biobase_2.14.0
[4] aroma.affymetrix_2.5.0 affxparser_1.26.4
aroma.apd_0.2.2
[7] R.huge_0.3.0 aroma.core_2.5.0
aroma.light_1.22.0
[10] BiocInstaller_1.2.1 matrixStats_0.5.0
R.rsp_0.7.5
[13] R.cache_0.6.2 R.filesets_1.1.5
digest_0.5.2
[16] R.utils_1.12.1 R.oo_1.9.3
affy_1.32.1
[19] R.methodsS3_1.2.2

loaded via a namespace (and not attached):
[1] affyio_1.22.0 DBI_0.2-5 IRanges_1.12.6
preprocessCore_1.16.0 RSQLite_0.11.1
[6] tools_2.14.1 zlibbioc_1.0.1

[Henrik Bengtsson]

Hi.

Yes, that won't work; HuGene-1_1-st-v1 and HuGene-1_0-st-v1 are
completely different chip types with incompatible CDFs.

It appears that Affymetrix does not provide a CDF for the
HuGene-1_1-st-v1 chip type. However, they do provide
HuGene-1_1-st-v1.r4.PGF and HuGene-1_1-st-v1.r4.CLF files (part of
their 'HuGene-1_1-st-v1_strip_libraryfile.zip' library file available
on their website). It should be possible to create a CDF from these
file. At the moment, there is not such support built into
aroma.affymetrix, but you could use the Perl scripts provided by
Elizabeth Purdom and Mark Robinson, see How To page 'Create a CDF file
from scratch (or from CLF and PGF files)'
[http://aroma-project.org/node/40].

Hope this helps

/Henrik

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[Henrik Bengtsson]

Actually, there is a much easier way to create the CDF; one can create
one from the corresponding PD package from Bioconductor. I did that
and made it available at:

http://aroma-project.org/chipTypes/HuGene-1_1-st-v1

A small disclaimer: I haven't verified it on real data, but similar
conversions have done before so everything "should be ok".

/Henrik