dear list, i'm working with the annotation package mogene10sttranscriptcluster.db for the Affy Mouse Gene 1.0 ST array and have the following two questions. one is that if i want to use the nsFilter() function to filter out control probes, with the older affy chips i'd something like: filteredEset <- nsFilter(eset, feature.exclude="^AFFX") but as far as i understand these newer chips do not have the prefix AFFX in the control probe names. all probe names i find in the annotation package above consist of numbers. so, i'd like to know if there is any easy way with nsFilter of excluding the control probes. the second questions is about failing to retrieve annotations for specific probe names, for instance, if i do the following: library(mogene10sttranscriptcluster.db) mogene10sttranscriptclusterENTREZID[["10566258"]] [1] NA i.e., i don't find annotation for probe 10566258, however if i download MoGene-1_0-st-v1.na30.mm9.transcript.csv from the NetAffx analysis center and grep this probe name i obtain the following entry: $ grep 10566258 MoGene-1_0-st-v1.na30.mm9.transcript.csv "10566258","10566258","chr7","-","110975048","110976443","26","ENSMUST 00000023934 // Hbb-b1 // hemoglobin, beta adult major chain // 7 E3|7 50.0 cM // 15129 /// AB364478 // Hbb-b2 // hemoglobin, beta adult minor chain // 7 E3|7 50.0 cM // 15130","ENSMUST00000023934 // ENSEMBL // Beta-globin gene:ENSMUSG00000052305 // chr7 // 100 // 100 // 26 // 26 // 0 /// AB364478 // GenBank // Mus musculus HBB2 mRNA for hemoglobin beta chain subunit, complete cds. // chr7 // 62 // 81 // 13 // 21 // 0 /// AB364477 // GenBank // Mus musculus HBB1 mRNA for hemoglobin beta chain subunit, complete cds. // chr7 // 52 // 81 // 11 // 21 // 0 /// AF071431 // GenBank // Mus musculus beta globin mRNA, partial cds. // chr7 // 40 // 19 // 2 // 5 // 0 [...etcetc] i'd like to know if this is a simple syncronization issue between NetAffx and this BioC annotation package and will get updated in the next release (i'm using the current BioC devel version just in case) or am i misusing the package and there is a way to retrieve the annotation? thanks!! sessionInfo() R version 2.11.0 Under development (unstable) (2009-10-06 r49948) x86_64-unknown-linux-gnu locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] mogene10sttranscriptcluster.db_4.0.1 org.Mm.eg.db_2.3.6 [3] RSQLite_0.7-3 DBI_0.2-4 [5] AnnotationDbi_1.9.2 Biobase_2.5.8