Entering edit mode
Hi,
I am the maintainer of oneChannleGUI. For data mining in my package I
have an implementation of IC coefficient derived from metaArray
package.
To run intcor function I use an Object of class mergeExpressionSet
created with two expression sets and the function mergeExprs:
> metaData
ExpressionSet (storageMode: list)
assayData: 31 features, 200 samples
element names: exprs
phenoData
sampleNames: GSM282373, GSM282374, ..., GSM282572 (200 total)
varLabels and varMetadata description:
Name: Name
FileName: FileName
Target: Target
featureData
featureNames: 200737_at, 200738_s_at, ..., AFFX-HUMGAPDH/M33197_M_at
(31 total)
fvarLabels and fvarMetadata description: none
experimentData: use 'experimentData(object)'
Annotation: hgu133a.db
ExpressionSet (storageMode: list)
assayData: 31 features, 204 samples
element names: exprs
phenoData
sampleNames: GSM308256, GSM308257, ..., GSM308460 (204 total)
varLabels and varMetadata description:
FileName: FileName
Target: Target
featureData
featureNames: 200737_at, 200738_s_at, ..., AFFX-HUMGAPDH/M33197_M_at
(31 total)
fvarLabels and fvarMetadata description: none
experimentData: use 'experimentData(object)'
Annotation:
to run intcor I use the metaArray function intcor:
merged.cor <- intcor(metaData)
At this point I get the following error:
Error in .C("intcor", as.double(unlist(expr)), as.integer(unlist(cl)),
:
C symbol name "intcor" not in DLL for package "metaArray"
If I run intCor from the MergeMaid package:
merged.cor <- intCor(metaData)
No errors are encountered.
It seems to me a problem in call of the C function.
Cheers
raffaele
>sessionInfo()
R version 2.9.0 (2009-04-17)
i386-pc-mingw32
locale:
LC_COLLATE=Italian_Italy.1252;LC_CTYPE=Italian_Italy.1252;LC_MONETARY=
Italian_Italy.1252;LC_NUMERIC=C;LC_TIME=Italian_Italy.1252
attached base packages:
[1] splines tools tcltk stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] MergeMaid_2.16.0 MASS_7.2-47 survival_2.35-4
[4] metaArray_1.20.0 oneChannelGUI_1.10.8 preprocessCore_1.6.0
[7] GOstats_2.10.0 RSQLite_0.7-1 DBI_0.2-4
[10] graph_1.22.2 Category_2.10.1 AnnotationDbi_1.6.1
[13] tkWidgets_1.22.0 DynDoc_1.22.0 widgetTools_1.22.0
[16] affylmGUI_1.18.0 affyio_1.12.0 affy_1.22.0
[19] limma_2.18.2 Biobase_2.4.1
loaded via a namespace (and not attached):
[1] annotate_1.22.0 genefilter_1.24.2 GO.db_2.2.11
GSEABase_1.6.1
[5] RBGL_1.20.0 XML_2.5-3 xtable_1.5-5
--
----------------------------------------
Prof. Raffaele A. Calogero
Bioinformatics and Genomics Unit
Dipartimento di Scienze Cliniche e Biologiche
c/o Az. Ospedaliera S. Luigi
Regione Gonzole 10, Orbassano
10043 Torino
tel. ++39 0116705417
Lab. ++39 0116705408
Fax ++39 0119038639
Mobile ++39 3333827080
email: raffaele.calogero at unito.it
raffaele[dot]calogero[at]gmail[dot]com
www: http://www.bioinformatica.unito.it
Info: http://publicationslist.org/raffaele.calogero
