[BioC] annotations of Human Gene 1.0 ST microarray and oneChannelGUI
ifig319 at ifi.csic.es
ifig319 at ifi.csic.es
Sun Aug 29 01:21:00 CEST 2010
Dear list,
This is my first experience working on microarray data. I am trying to
analyze Human Gene 1.0 ST microarray data with oneChannelGUI. However,
this seems to be not a straightforward task. I have been playing
around with data and the application and I am a little bit confused
and without any result yet!
First, I installed all the packages and then, followed the user guide
instructions.
When I select "GENE 1.0 ST ARRAYS: probe sets summary from Affymetrix
APT" option to perform a new analysis, it asks me if I want to use APT
for gene/exon summaries. I click "yes" and chose the organisms (in my
case, Hs). Next, I select the working directory, the target file and
answer "no" to the question "are you using genechips version 1.1?".
Finally, as APT tool intensity summary option, I select "rma-sketch".
Inmmediatly, I get a series of error messages (see below).
I really do not know what is happening here. I would like to make the
background correction, normalization and summarization, and also run
limma.
On the other hand, I can load a normalized tab delimited data set and
apply some functions on it, but I do not know how to include the
annotations into the final list of differential expressed genes (top
table).
anybody has a suggestion about what is happening here and how could I
solve it?
I would appreciate your help.
Best regards and thank you in advance for your attention.
Virginia.
-------
R CONSOLE:
Gene level probe sets summary started
Gene level probe sets summary ended
Error en as.matrix(my.exons) :
ninguna función desde donde volver, saltando a nivel superior
Además: Mensajes de aviso perdidos
1: In file(file, "rt") :
sólo fue usado el primer elemento del argumento 'description'
2: In system(gene.rma.sketch, wait = T) : C:/Archivos no encontrado
3: In file(file, "rt") :
no fue posible abrir el archivo 'C:/onChannelGUI/out5f906952/': No
such file or directory
>
> sessionInfo()
R version 2.11.1 (2010-05-31)
i386-pc-mingw32
locale:
[1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252
[3] LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C
[5] LC_TIME=Spanish_Spain.1252
attached base packages:
[1] grid tools tcltk stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] oneChannelGUI_1.14.6 RaExExonProbesetLocation_1.0.0
[3] MoExExonProbesetLocation_1.0.0 HuExExonProbesetLocationHg19_0.0.2
[5] Genominator_1.2.0 GenomeGraphs_1.8.0
[7] biomaRt_2.4.0 edgeR_1.6.13
[9] IRanges_1.6.15 preprocessCore_1.10.0
[11] GOstats_2.14.0 RSQLite_0.9-2
[13] DBI_0.2-5 graph_1.26.0
[15] Category_2.14.0 AnnotationDbi_1.10.2
[17] tkWidgets_1.26.0 DynDoc_1.26.0
[19] widgetTools_1.26.0 affylmGUI_1.22.0
[21] affyio_1.16.0 affy_1.26.1
[23] limma_3.4.4 Biobase_2.8.0
loaded via a namespace (and not attached):
[1] annotate_1.26.1 genefilter_1.30.0 GO.db_2.4.1 GSEABase_1.10.0
[5] RBGL_1.24.0 RCurl_1.4-3 splines_2.11.1 survival_2.35-8
[9] XML_3.1-1 xtable_1.5-6
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