Data Set 02/15

Hi Juan

Here are the original files Shabnam used. It seems that vsn_normalization.xls is the original file, so you might want to write your own script to extract the gene time profiles from that one directly. Please rerun the F vs K plots with these.

Please can you also check that the gene names in top50.xls are actually the genes in the right hand column of top50®.sif?

Thanks

David


-----Original Message-----
From: Shabnam Moobedmehdiabadi
Sent: Wed 2/14/2007 15:04
To: David Wild
Cc:
Subject: Data Sets

Dear David,

The vsn-normalization file is the original normalized data with 2 technical replicates each has 3 rep. I used combine.m script to combine the data to have 6 rep for each gene. I saved the result in timecourse.xls file. I used timecourse.xls file for timecourse analysis finding the HotellingT2 value for each gene.
the ready.xls file is timecourse.xls file which has been sorted on HotellingT2 value. I used the top 50 genes in ready.xls file for vbssm training which I saved them in top50.xls. this is the file that I used to produce figure 3 in the NSF report. normalize.xls is the same data but I did standard normalized transform as well.

About the new set of genes 50genes+regulators, I extracted the genes and the relative expressions from timecourse.xls files and I saved it as ready_top50&reg.xls (in alphabetical order). I extracted the 50genes+regulators name from top50®.sif (which is the same as the figure in networktop50&reg.tiff ) file as you sent to me. As I examined the genes names I figured out that the Yellow circles genes in networktop50&reg.tiff are the same genes as in top50.xls file but the with circles are not included in top50.xls file.

Please let me know if my explanations are not clear.

Best regards,
Shabnam