Hi I am reliatevely new to R and BioC and have so far been using the package limma to analyse my microarray data. I have got to the stage where I have some interesting features and want to use the respective IDs of these to extract gene data from additional tables within R. Top table data: Block Row Column ID Name M A t P.Value adj.P.Val B 16415 28 9 15 I6481_cpg298I7 13_108590257-108591866 3.761146 12.28307 23.07024 1.418257e-16 4.068837e-12 27.90629 Gene info table: V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 1 I1 1 828862 830900 function 68.2 0.717 <na> <na> <na> 2 I2 1 847313 850747 function 69.9 0.717 ENSG00000187634 850393:870375:1 SAMD11 The problem is neither contains exactly the same data in the same order, and the IDs in the Top table are extended relative to those in the 2nd table eg I6481_cpg29817 in the Top table is simply I6481 in the genes data table. So far I have tried various looping grep scripts to use the IDs from one table to give me positions in the other - to no avail!! I think this is probably a fairly trivial problem, but I am starting to loose hair over this!! Any help would be greatly appreciated. Thanks Rob Illingworth

Hi Rob! Is the number of rows the same in each table?In other words do both the tables contain the same genes/spots? Is the identifier of the second table eg I6481 unique (in other words no matter the second part of the identifier in the Top Table, is the first part unique and enough to identify the spot)? If the answer in both questions is yes then just do pos<-order(toptable[,5]) TopTable2<-toptable[pos,] And pos<-order(geneinfotable[,<the column="" that="" has="" the="" gene="" identifiers="">]) geneinfotable2<-geneinfotable[pos,] Now both the tables have the spots in the same order! Niki ICB Swann Building The King's Buildings University of Edinburgh Edinburgh, EH9 3JR Scotland UK tel:(0044)0131-6507072 fax:(0044)0131-6505379 R.Athanasiadou at sms.ed.ac.uk -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of RS Illingworth Sent: 03 May 2007 15:47 To: bioconductor at stat.math.ethz.ch Subject: [BioC] Using Top Table to extract gene info from additional tablewithin Hi I am reliatevely new to R and BioC and have so far been using the package limma to analyse my microarray data. I have got to the stage where I have some interesting features and want to use the respective IDs of these to extract gene data from additional tables within R. Top table data: Block Row Column ID Name M A t P.Value adj.P.Val B 16415 28 9 15 I6481_cpg298I7 13_108590257-108591866 3.761146 12.28307 23.07024 1.418257e-16 4.068837e-12 27.90629 Gene info table: V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 1 I1 1 828862 830900 function 68.2 0.717 <na> <na> <na> 2 I2 1 847313 850747 function 69.9 0.717 ENSG00000187634 850393:870375:1 SAMD11 The problem is neither contains exactly the same data in the same order, and the IDs in the Top table are extended relative to those in the 2nd table eg I6481_cpg29817 in the Top table is simply I6481 in the genes data table. So far I have tried various looping grep scripts to use the IDs from one table to give me positions in the other - to no avail!! I think this is probably a fairly trivial problem, but I am starting to loose hair over this!! Any help would be greatly appreciated. Thanks Rob Illingworth _______________________________________________ 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