Hi, I have a question when using this package. Some candidate microRNA targets seem to be missing. Here is an example. I searched through the TargetScan website, and found that "hsa-miR-939" has a candidate target "CYFIP2". This gene is represented by at least one probe "A_23_P156117". I couldn't find this relationship using RmiR. Don't know whether I missed something. I made a toy example here. > library(hgug4112a.db) > library(annotate) > lookUp("A_23_P156117","hgug4112a","SYMBOL") $A_23_P156117 [1] "CYFIP2" > genes = data.frame(genes=c("A_23_P156117", "A_23_P352870"), expr=c(-1.3, 1.5)) > mirna = data.frame(mirna=c("hsa-miR-939", "hsa-miR-630"), expr=c(1.1, 1.3)) > library(RmiR) Loading required package: RmiR.Hs.miRNA Loading required package: RSVGTipsDevice > comb = read.mir(genes=genes, mirna=mirna, annotation="hgug4112a.db", id.out="probes", at.least=1) Error in `$<-.data.frame`(`*tmp*`, "mirCV", value = NA) : replacement has 1 rows, data has 0 > > sessionInfo() R version 2.10.0 (2009-10-26) x86_64-redhat-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] RmiR_1.2.0 RSVGTipsDevice_1.0-1 RmiR.Hs.miRNA_1.0.6 [4] annotate_1.24.0 hgug4112a.db_2.3.6 org.Hs.eg.db_2.3.6 [7] RSQLite_0.7-3 DBI_0.2-4 AnnotationDbi_1.8.1 [10] Biobase_2.6.1 loaded via a namespace (and not attached): [1] xtable_1.5-6 > Jason [[alternative HTML version deleted]]