Dear List

I wonder if any of you may have used package "FLUSH.LVS.bundle" with
Affymetrix Gene 1.0 ST arrays. I get an error when processing the RA object.
I supose this error is related because initially was designed to use with
arrays with mm probes, but in principle you can use without it, for the
moment I cannot handle to solve it, but I think the solution may be
possible. Here is the code and the error I get.

Thank you very much.

library("affy")
library("FLUSH.LVS.bundle")
data <- ReadAffy()
RA.fit <- compute.RA(data)

Fitting models
|                    |
|#Error in t(contr.helmert(nprobes)) :
  error in evaluating the argument 'x' in selecting a method for function
't'

traceback()
6: t(contr.helmert(nprobes))
5: as.vector(data)
4: matrix(rep(t(contr.helmert(nprobes)), nsamples), byrow = T, ncol =
nprobes -
       1)
3: make.design(nsamples = nsamples, nprobes = tabProbes[i])
2: compute.RA(data)
1: compute.RA(data)

sessionInfo()

R version 2.12.0 (2010-10-15)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=ca_ES.utf8       LC_NUMERIC=C
 [3] LC_TIME=ca_ES.utf8        LC_COLLATE=ca_ES.utf8
 [5] LC_MONETARY=C             LC_MESSAGES=ca_ES.utf8
 [7] LC_PAPER=ca_ES.utf8       LC_NAME=C
 [9] LC_ADDRESS=C              LC_TELEPHONE=C
[11] LC_MEASUREMENT=ca_ES.utf8 LC_IDENTIFICATION=C

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

other attached packages:
[1] hugene10stv1cdf_2.7.1  FLUSH.LVS.bundle_1.3.1 affyPLM_1.26.0
[4] preprocessCore_1.12.0  gcrma_2.22.0           quantreg_4.53
[7] SparseM_0.86           affy_1.28.0            Biobase_2.10.0

loaded via a namespace (and not attached):
[1] affyio_1.18.0        AnnotationDbi_1.12.0 Biostrings_2.18.2
[4] DBI_0.2-5            IRanges_1.8.4        RSQLite_0.9-4
[7] splines_2.12.0       tools_2.12.0

Oriol Senan Campos
Non Linear Dynamics Non Linear Optics Group
Universitat Politècnica de Catalunya, Campus de Terrasa
* +34 93 739 *8835

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