search for: drosophila2

...naffy analysis but can¹t find what is the name of the annotation file I need to use. Here is the output of the AffyBatch object I am using: > expData AffyBatch object size of arrays=732x732 features (16749 kb) cdf=Drosophila_2 (18952 affyids) number of samples=4 number of genes=18952 annotation=drosophila2 So when I try to use and annaffy procedure I get: >Symbol = aafSymbol(geneIDs, "drosophila2") [1] "You are missing drosophila2 looking to see if it is available." Error in chkPkgs(chip) : couldn''t find function "userQuery" In the documentation it is spec...

...2 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] lattice_0.19-13 drosophila2.db_2.4.5 org.Dm.eg.db_2.4.6 [4] GOstats_2.16.0 RSQLite_0.9-4 DBI_0.2-5 [7] graph_1.28.0 Category_2.16.0 AnnotationDbi_1.12.0 [10] xtable_1.5-6 GEOquery_2.16.3 ellipse_0.3-5 [13] RColorBrewer_1.0-2 hopach_2.10.0 cluster_1.13.2 [16] limma_3.6.9...

Hi everybody, I have a problem when trying to do the quality control with the packages simpleaffy and affyQCReport with the drosophila chip 2.0 At first I got the messeage, that the *.qcdef file is not there. I followed the instructions in tha manual and created the file like that: array drosophila2cdf alpha1 0.05 alpha2 0.065 spk bioB AFFX-r2-Ec-bioB-3_at spk bioC AFFX-r2-Ec-bioC-3_at spk bioD AFFX-r2-Ec-bioD-3_at spk creX AFFX-r2-P1-cre-3_at ratio actin3/actin5 AFFX-Dros-ACTIN_3_at AFFX-Dros-ACTIN_5_at ratio actin3/actinM AFFX-Dros-ACTIN_3_at AFFX-Dros-ACTIN_M_f_at ratio gapdh3/gapdh5 AFFX-D...