search for: totable

....At.tairGENENAME[ids] #map the probe ids to the gene names in TAIR The output of which is AnnDbBiMap[1] number<-org.At.tairENTREZID[ids] #map the probe ids to the gene ids in TAIR The output of which is AnnDbBiMap[1] And then I try to merge both the lists as : xx<-toTable(entrez) yy<-toTable(number) complete<-merge(xx,yy) I get an error in this step and unable to proceed further.The error reads: Error in fix.by(by.y.y): 'by' must specify uniquely valid column(s) Is it because ids <- scr[,1] is a factor ? How would it be possible...

Hi All, I have an CBS segmentation algorithm output for 10 tumor samples each from 2 different tumors. Now, I am in an urgent need to assign gene (followed by all genes present) that belong to a particular segment after I removed all the CNVs from segment data. The format of the data is: Sample Chromosome Start End Num_Probes Segment_Mean Sample1A-TA 1 51598 76187 15

Hi, is there any package/function in Bioconductor that can do this: if given the chromosome positions of a fragment, find out all genes within, and with the information about which strand is the sense strand. And vice versa. Thanks a lot. ----- Appreciate your time & attention! -- View this message in context: http://www.nabble.com/list-genes-w-n-a-genomic-fragment-tp18331452p18331452.html

I am trying to use apply and a list to supply names to a set of tables I want to generate. Below is an example that I hope mimics the larger original problem. EXAMPLE aa <- c( 2,2,1,1,2) bb <- c(5,6,6,7,4) aan <- c("yes", "no") bbn <- c("a", "b", "c", "d") mynames <- c("abby", "billy") mylist <-

Dear All, I need to fetch GO ontologies for Homo sapiens with their mappings to corresponding Uniprot identifiers. I would be using this information to compare result from a clustering algorithm with existing protein complexes. This would be a test to check how the clustering algorithm accurately captures GO terms with respect to the known protein complexes. Can anyone suggest a simple workflow