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]]

