You are correct. That is the list of terms associated with the SPARC- like 1 gene. ________________________________ From: Laya Rose [roselaya98@gmail.com] Sent: Friday, 19 April 2013 19:09 To: Dario Strbenac Subject: Re: [BioC] Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 1 did not have 4 elements Sir i have a doubt in this > tbl <- toptable(blood_ebFit,coef=1) > ids <- tbl[["ID"]] > ids <- c("212624_s_at","200795_at","203797_at","202508_s_at","218309 _at","212233_at","203130_s_at","202260_s_at","205237_at","209072_at"," 214247_s_at","209469_at","204971_at","209074_s_at","204471_at","204337 _at","204992_s_at","209170_s_at","213975_s_at","203001_s_at","201387_s _at","215116_s_at","221805_at","203999_at","218332_at","203540_at","21 0198_s_at") > library("hgu133a.db") > entrez <- hgu133aENTREZID[ids] > toTable(entrez) probe_id gene_id 1 200795_at 8404 2 201387_s_at 7345 3 202260_s_at 6812 4 202508_s_at 6616 5 203001_s_at 11075 6 203130_s_at 3800 7 203540_at 2670 8 203797_at 7447 9 203999_at 6857 10 204337_at 5999 11 204471_at 2596 12 204971_at 1475 13 204992_s_at 5217 14 205237_at 2219 15 209072_at 4155 16 209074_s_at 11170 17 209170_s_at 2824 18 209469_at 2823 19 210198_s_at 5354 20 212233_at 4131 21 212624_s_at 1123 22 213975_s_at 4069 23 214247_s_at 27122 24 215116_s_at 1759 25 218309_at 55450 26 218332_at 55859 27 221805_at 4747 > genename <- hgu133aGENENAME[ids] > merge(toTable(entrez), toTable(genename)) probe_id gene_id gene_name 1 200795_at 8404 SPARC-like 1 (hevin) 2 201387_s_at 7345 ubiquitin carboxyl-terminal esterase L1 (ubiquitin thiolesterase) 3 202260_s_at 6812 syntaxin binding protein 1 4 202508_s_at 6616 synaptosomal- associated protein, 25kDa 5 203001_s_at 11075 stathmin-like 2 6 203130_s_at 3800 kinesin family member 5C 7 203540_at 2670 glial fibrillary acidic protein 8 203797_at 7447 visinin-like 1 9 203999_at 6857 synaptotagmin I 10 204337_at 5999 regulator of G-protein signaling 4 11 204471_at 2596 growth associated protein 43 12 204971_at 1475 cystatin A (stefin A) 13 204992_s_at 5217 profilin 2 14 205237_at 2219 ficolin (collagen/fibrinogen domain containing) 1 15 209072_at 4155 myelin basic protein 16 209074_s_at 11170 family with sequence similarity 107, member A 17 209170_s_at 2824 glycoprotein M6B 18 209469_at 2823 glycoprotein M6A 19 210198_s_at 5354 proteolipid protein 1 20 212233_at 4131 microtubule- associated protein 1B 21 212624_s_at 1123 chimerin (chimaerin) 1 22 213975_s_at 4069 lysozyme 23 214247_s_at 27122 dickkopf 3 homolog (Xenopus laevis) 24 215116_s_at 1759 dynamin 1 25 218309_at 55450 calcium/calmodulin-dependent protein kinase II inhibitor 1 26 218332_at 55859 brain expressed, X-linked 1 27 221805_at 4747 neurofilament, light polypeptide > goIds <- mappedRkeys(hgu133aGO[ids[1]]) > library("GO.db") > head(as.data.frame(Term(goIds))) Term(goIds) GO:0007264 small GTPase mediated signal transduction GO:0008045 motor axon guidance GO:0032314 regulation of Rac GTPase activity GO:0048013 ephrin receptor signaling pathway GO:0050770 regulation of axonogenesis GO:0051056 regulation of small GTPase mediated signal transduction > goIds <- mappedRkeys(hgu133aGO[ids[2]]) > head(as.data.frame(Term(goIds))) Term(goIds) GO:0007165 signal transduction GO:0005578 proteinaceous extracellular matrix GO:0005615 extracellular space GO:0005509 calcium ion binding > the result got from the script head(as.data.frame(Term(goIds))), do all of them are the pathways of the corresponding gene? On Fri, Apr 12, 2013 at 3:57 PM, Laya Rose <roselaya98@gmail.com<mailto:roselaya98@gmail.com>> wrote: thank u sir On Fri, Apr 12, 2013 at 12:29 PM, Dario Strbenac <d.strbenac@garvan.org.au<mailto:d.strbenac@garvan.org.au>> wrote: Your metadata file is in the wrong format. The first column should not have any heading. -- Laya Rose -- Laya Rose [[alternative HTML version deleted]]