Entering edit mode
Oriol SENAN
▴
10
@oriol-senan-4395
Last seen 10.1 years ago
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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