Hi All, Using the package ConnectivityMap, the data "rankMatrix" represents instances such as inst_1, inst_2, ..., inst_6100 for each gene. I am a bit confused, what exactly such instances mean and how they are computed? If they represent the difference between perturbation and vehicle samples, why they all are positive? I assume we may have at least some negative values for some genes( like down-regulated genes). I tried to download the dataset GSE5258, titled with "Connectivity Map dataset (build01)" refereed in the supplemental material of the paper "The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease" from GEO. For example the expression value of the gene "1007_s_at" for the sample "EC2003090503AA" (perturbation_scan_id) is 387.6, while for the same gene this value for sample "EC2003090502AA" (vehicle_scan_id3) is 393.2. By looking at the matrix rankMatrix in ConnectivityMap package for the same gene "1007_s_at", we have some instances from inst_1 to inst_6100. I don't understand that how these instance values for the gene "1007_s_at" come up? As an example, for this gene, we have instance values such as 6432, 12201 for inst_1 and inst_2. What is the relationship between such samples and sample values in dataset GSE5258? Thank You, Azam [[alternative HTML version deleted]]

Hi Azam, Your best bet for exploring these questions is to contact the Connectivity Map project at the Broad, which is the source of the data: http://www.broadinstitute.org/cmap/ Sorry that I cannot be more directly helpful. - Paul On Jun 24, 2014, at 8:39 PM, "Azam" <azam.peyvand at="" gmail.com=""> wrote: > Hi All, > > Using the package ConnectivityMap, the data "rankMatrix" represents instances such as inst_1, inst_2, ..., inst_6100 for each gene. > I am a bit confused, what exactly such instances mean and how they are computed? > > If they represent the difference between perturbation and vehicle samples, why they all are positive? I assume we may have at least some negative values for some genes( like down-regulated genes). > > I tried to download the dataset GSE5258, titled with "Connectivity Map dataset (build01)" refereed in the supplemental material of the paper "The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease" from GEO. > > For example the expression value of the gene "1007_s_at" for the sample "EC2003090503AA" (perturbation_scan_id) is 387.6, while for the same gene this value for sample "EC2003090502AA" (vehicle_scan_id3) is 393.2. > > By looking at the matrix rankMatrix in ConnectivityMap package for the same gene "1007_s_at", we have some instances from inst_1 to inst_6100. > I don't understand that how these instance values for the gene "1007_s_at" come up? As an example, for this gene, we have instance values such as 6432, 12201 for inst_1 and inst_2. > What is the relationship between such samples and sample values in dataset GSE5258? > > Thank You, > Azam