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","210198_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


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