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 funci?n desde donde volver, saltando a nivel superior Adem?s: Mensajes de aviso perdidos 1: In file(file, "rt") : s?lo 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