Hi Rosienne, we agree it would be nice to have the 1 row per gene output when just having gene_ids in the output. People have wanted this for a while so we just need to come up with a technical solution: the obvious one of just selecting distinct rows from the database can be a bit slow for large datasets.
in a old incarnation of mart we did used to report the rows for "not found" IDs so it would be nice to reintroduce this feature. We will look into this and hopefully get something in for the next release Best wishes Damian On Thu, 22 Feb 2007, Rosienne wrote: > Hi, > > a few weeks ago I was attending an Open Door Workshop at the Sanger. I > had occasion to speak to one of your team and mention a couple of > problems we regularly encounter when using biomart. I was advised to > post to this address. > > > I, and my colleagues, use biomart to output gene related information > for lists of microarray feature IDs. Even though we untick the ensembl > transcript ID box we still get an output for each transcript. In some > cases, where genes have 9 documented transcripts we get 9 perfectly > replicated entries. When dealing with lists of over a thousand genes > each time this gets very confusing and generally makes excel stop > responding! > > We wonder if in future re-works of the tool a gene specific rather than > a transcript specific output can be made available. We are aware that > for people working on only one, or a handful of genes, getting all the > transcript specific information is essential. However, it would make > life a lot easier for scientists like us who handle large gene lists > if we could specifically select to obtain only gene specific outputs, 1 > gene = 1 row of output. > > Our second major problem stems from the fact that sometimes there is no > information linked to particular microarray feature IDs. The count tab > tells you how many out of your list were found but there is no > information whatsoever about the ones that were not found. Manually > finding which 50 out of a list of 1000 were not found is not easy. An > output list of features not found, or inclusion of the not found items > within the output with a short 'not found' comment next to them would > be very useful. > > > In summary, for us the ideal situation would be if we could input a > list of 1000 feature IDs and as output get a list of 1000 rows, 1 gene > per row, in the same sequence as the input list, with either empty > cells or a not found comment against those not found. > > > > Besides this particular feature, biomart is great and has made data > mining of large data sets so much more accessible! > Thank you. > > > Regards > Rosienne > _______________________________________________________ > Rosienne Farrugia > Division of Transfusion Medicine > Department of Haematology > University of Cambridge > Long Road > Cambridge > CB2 2PT > > Tele: 01223 548008 > Fax: 01223 548136 >
