Dear Xi yes, the code should be: library("org.Hs.eg.db") uu = as.list( revmap(org.Hs.egMAP) ) i = grep("^1q", names(uu)) uu[i] I get a list with 106 elements, and 1796 unique Entrez-IDs: > head(uu[i]) $`1q` [1] "4030" "7254" "100113374" "100302291" "100313962" $`1q12` [1] "2369" "9557" "9659" "9939" "11243" "27444" [7] "29765" "114814" "171419" "401131" "644450" "100270895" $`1q12-q21` [1] "10262" "10903" $`1q12-q21.2` [1] "25832" $`1q12-q22` [1] "6063" $`1q12-q23` [1] "1805" "4002" "4209" > length(unique(unlist(uu[i]))) [1] 1796 sessionInfo() as below - i.e. the same version of org.Hs.eg.db, 2.4.1, as you use. I have no idea why you only get 5 Entrez-IDs. What is the value of 'i' in your session after running the code above? Can you try again, from a clean R session, just to make sure there are no typos / remnants of previous expressions? And, yes, I do think that the notation `1q12` means that the gene is on chromosome 1q, and it is not separately annotated in the `1q` list element. The creator of the "org.Hs.eg.db" package might have more insight here. Best wishes Wolfgang Xi Zhao scripsit 08/09/10 11:46: > > Dear Huber, > > Thanks for replying. I I still have problem retrieving the entrez genes > on the chromosome sub-arm, such as 1q, 16q. > > By running the sample code you gave, I retrieved 5 genes locate on "1q", > but isn?t "1q" supposed refer to the whole q arm of chromosome 1, which > should harbor >> than 5 genes... > uu = as.list( revmap(org.Hs.egMAP) ) > i = grep("^1q", names(uu)) > uu[i] > $`1q` > [1] "4030" "7254" "100113374" "100302291" "100313962" > > Look at 16q from the results by GOstats, there are 357 genes from 16q > (appeared in my array), but revmap(org.Hs.egMAP) only gives 5 genes on > 16q. Does the notation "16q" not mean the whole q arm on chr 16 but only > a cytoband in package "org.Hs.eg.db"?? > > id Pvalue OddsRatio ExpCount Count Size > Chr 16q 1.210938e-88 20.332155 10.038699 113 357 > >> get("16q", revmap(org.Hs.egMAP)) > [1] "8136" "140454" "171013" "100125393" "100303743" > > And I guess by library("org.Hs.egCHR") you meant library("org.Hs.eg.db")? > > Thanks again! > Xi > > > > > R version 2.11.1 (2010-05-31) > x86_64-apple-darwin9.8.0 > > locale: > [1] C > > attached base packages: > [1] tcltk grid stats graphics grDevices utils datasets methods > [9] base > > other attached packages: > [1] humanCHRLOC_2.1.6 GO.db_2.4.1 org.Hs.eg.db_2.4.1 > [4] qvalue_1.22.0 GOstats_2.14.0 RSQLite_0.9-1 > [7] DBI_0.2-5 graph_1.26.0 Category_2.14.0 > [10] AnnotationDbi_1.10.1 Biobase_2.8.0 ggplot2_0.8.8 > [13] proto_0.3-8 reshape_0.8.3 plyr_1.0.3 > > loaded via a namespace (and not attached): > [1] GSEABase_1.10.0 RBGL_1.24.0 XML_3.1-0 annotate_1.26.0 > [5] genefilter_1.30.0 splines_2.11.1 survival_2.35-8 tools_2.11.1 > [9] xtable_1.5-6 > > > > On Sep 8, 2010, at 10:41 AM, Wolfgang Huber wrote: > >> Dear Xi, >> >> try this: >> >> library("org.Hs.egCHR") >> uu = as.list( revmap(org.Hs.egMAP) ) >> print(uu) >> i = grep("^1q", names(uu)) >> uu[i] >> >> length(unique(unlist(uu[i]))) >> # [1] 1796 >> >> >> > sessionInfo() >> R version 2.12.0 Under development (unstable) (2010-09-07 r52876) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=la_AU.utf8 LC_NUMERIC=C >> [3] LC_TIME=la_AU.utf8 LC_COLLATE=la_AU.utf8 >> [5] LC_MONETARY=C LC_MESSAGES=la_AU.utf8 >> [7] LC_PAPER=la_AU.utf8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=la_AU.utf8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] org.Hs.eg.db_2.4.1 RSQLite_0.9-2 DBI_0.2-5 >> [4] AnnotationDbi_1.11.4 Biobase_2.9.0 fortunes_1.3-7 >> >> loaded via a namespace (and not attached): >> [1] tools_2.12.0 >> >> >> Xi Zhao scripsit 08/09/10 10:10: >>> >>> Dear list, >>> >>> Im struggling retrieving the full list of the entrez geneIDs for each >>> of the enriched chromosome bands (obtained by "GOstats"). >>> >>> revmap(org.Hs.egCHR) doesnt give the entrezIDs for the sub-arms, only >>> for the whole arm: >>> >>> mget(c("16", "1q"), revmap(org.Hs.egCHR), ifnotfound=NA) # Map >>> between Entrez Gene IDs and Chromosomes >>> $`1q` >>> [1] NA >>> >>> revmap(org.Hs.egMAP) only gives a few genes locate on that >>> chromosome... (or did I do it wrong?) >>> >>> mget(c("16", "1q"), revmap(org.Hs.egMAP), ifnotfound=NA) # Map >>> between Entrez Gene Identifiers and cytogenetic maps/bands >>> $`16` >>> [1] "8720" >>> $`1q` >>> [1] "4030" "7254" "100113374" "100302291" "100313962" >>> >>> Any suggestion / hint is appreciated! >>> >>> Kindest regards, >>> Xi >>> >>> >>> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch <mailto:bioconductor at="" stat.math.ethz.ch=""> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> -- >> >> >> Wolfgang Huber >> EMBL >> http://www.embl.de/research/units/genome_biology/huber >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber