Hello, everyone.
Thanks in advance.
I'm just beginning in bioinformatics, so any help would be really appreciated.
I want to compare the gene expression values between L1000 signature in GCT format data and log2(foldchange) values for specific gene expression data.I knew that L1000 measurement and interred epression values are as similar with RNA-seq as RNA-seq is with Affymetrix, and it was shown by figure 1.e in L1000 paper, 2017.
But i want to find that it is a proper method to compare directly between L1000 landmark genes expression value for specific dose and length of time that a perturbagen was applied to the cells.
For example, if landmark gene PSME1 have a signature value for 3.6 at 6 h 3microM in cell line A375 and have a log2(foldchange) value for 2.0, is it right to compare two values which are 2.0 and 3,6? Also is it right to make a decision that the PSME1 is up-regulated gene(or over expressed gene) at two expression data?
Moreover, i calculated a average gene signature values for each genes, if the signature pert_idose and pert_itime is same to compare with log2(foldchange) values. Is it a right method that get a average signature value for landmark gene at same pert_itime and pert_idose ?
Again, thank you so much
Dear @sslimb95, Did you find your answer. If you did, please do update the answer as several people also have the same qs.