[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  
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  
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  
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.


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)

[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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