Thanks for reverting back Brooke. Here is the link of the original dataset (Human U133A + GNF1H (gcRMA-condensed) GeneAtlas (7M)):
http://wombat.gnf.org/downloads/gnf1h,gcrma.zip or can be navigated from the main page: http://wombat.gnf.org/index.html In addition to my previous question, I don't quite understand what exact operations UCSC-GB has done to transform the original GNF data (in record #1 below) to various other forms (records #2, #3, #4 below) (for clarity I am copying the records again): 1. From GNF (Novartis) site (one value for each of the 79 tissues (probably avergaed over the two measurement?) - looks like raw scores?) 208553_at 8.3 6.3 6.55 5.35 6.35 6.55 5.1 8.05 6.4 6.9 7.8 7.75 9.8 8.85 8.35 8 8.9 7.35 7.8 9.65 5.55 6.85 5 5.1 6.05 6.7 4.6 6.7 6.75 5.7 5.9 5.4 6.5 7.15 4.8 8.1 6.5 6.45 6.5 7.65 5.9 8.2 8.75 6.15 5.75 5.35 4.45 4.95 7 6.45 7.4 6.8 6.2 7.65 7.4 5.9 6.9 5.4 7.65 6.65 6.4 5.7 6.05 6.25 5.3 6.65 5.65 5.95 6.15 6.8 7.65 6.45 6.75 5.6 5.6 7.1 5.65 6.95 5.6 2. UCSC Table: gnfHumanAtlas2All (2 measurements each in 79 tissues) 208553_at 158 38,15,27,48,201,25,361,23,156,491,383,420,49,328,76,68,664,406,330,139,331,224,58,42,217,53,62,28,38,23,25,100,324,191,53,30,29,49,15,56,67,29,96,72,93,54,25,34,110,81,118,24,38,25,25,69,17,15,82,36,59,32,13,55,22,29,76,70,16,32,120,29,208,18,86,37,26,42,31,23,48,24,30,38,66,48,63,45,53,68,31,30,38,44,59,28,22,31,38,95,25,26,34,21,18,85,58,29,17,28,17,38,35,13,75,81,47,23,253,23,55,131,88,18,82,18,24,46,40,95,19,61,16,32,60,28,24,91,19,79,29,50,47,53,29,68,55,34,110,60,69,108,26,43,23,22,72,83, 3. UCSC Table: gnfHumanAtlas2AllRatio (2 measurements each in 79 tissues) 208553_at 158 -0.291,-2.217,-0.784,0.046,2.112,-0.895,2.957,-1.016,1.746,3.400,3.042,3.175,0.076,2.818,0.709,0.548,3.836,3.126,2.827,1.580,2.832,2.268,0.319,-0.147,2.222,0.189,0.415,-0.732,-0.291,-1.016,-0.895,1.105,2.801,2.038,0.189,-0.632,-0.681,0.076,-2.217,0.268,0.527,-0.681,1.046,0.631,1.000,0.216,-0.895,-0.452,1.242,0.801,1.343,-0.954,-0.291,-0.895,-0.895,0.569,-2.217,-2.217,0.818,-0.369,0.343,-0.539,-2.217,0.242,-1.080,-0.681,0.709,0.590,-2.217,-0.539,1.368,-0.681,2.161,-2.217,0.887,-0.330,-0.839,-0.147,-0.585,-1.016,0.046,-0.954,-0.632,-0.291,0.505,0.046,0.438,-0.047,0.189,0.548,-0.585,-0.632,-0.291,-0.080,0.343,-0.732,-1.080,-0.585,-0.291,1.031,-0.895,-0.839,-0.452,-1.147,-2.217,0.870,0.319,-0.681,-2.217,-0.732,-2.217,-0.291,-0.410,-2.217,0.690,0.801,0.015,-1.016,2.444,-1.016,0.242,1.494,0.920,-2.217,0.818,-2.217,-0.954,-0.016,-0.217,1.031,-2.217,0.392,-2.217,-0.539,0.368,-0.732,-0.954,0.969,-2.217,0.765,-0.681,0.105,0.015,0.189,-0.681,0.548,0.242,-0.452,1. 242,0.368,0.569,1.216,-0.839,-0.113,-1.016,-1.080,0.631,0.836, 4. UCSC Table: gnfAtlas2 (one value for each of the 79 tissues (probably averaged over the two measurements in the same tissue)) 785 chr6 26264597 26265257 208553_at 998 + 26264597 26265257 0 1 660, 0, 79 0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78, -0.454000,-2.217000,-0.673000,0.224000,0.649000,-0.881000,0.278000,-0.593000,0.195000,-0.988000,-1.378000,0.344000,-0.028000,-0.163000,1.022000,-1.048000,-0.493000,-0.098000,-0.800000,-0.726000,-0.288000,-0.105000,-0.067000,-0.222000,-0.303000,-0.975000,0.608000,0.839000,0.609000,2.204000,2.550000,-0.369000,2.573000,0.970000,3.108000,1.447000,0.629000,3.481000,0.086000,1.206000,-0.159000,-0.653000,0.105000,2.420000,-1.254000,-0.182000,0.008000,-1.254000,0.370000,-0.833000,0.734000,-0.462000,-0.913000,-0.185000,-0.485000,-1.314000,0.746000,0.102000,0.196000,-0.673000,0.805000,-0.476000,-0.181000,-0.194000,0.892000,0.407000,-1.474000,-0.867000,0.276000,-0.609000,-0.077000,0.369000,-0.799000,-0.501000,0.714000,0.868000,-0.649000,-0.700000,-1.378000, Thanks a lot, Raj --- On Thu, 6/11/09, Brooke Rhead <[email protected]> wrote: > From: Brooke Rhead <[email protected]> > Subject: Re: [Genome] GNF Atlas 2 data > To: "Raj" <[email protected]> > Cc: [email protected] > Date: Thursday, June 11, 2009, 12:30 AM > Hello Raj, > > Can you please point me to the location of the gene > expression record on the GNF site? > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > On 06/10/09 10:33, Raj wrote: > > > > Hi, > > > > Below are two gene expression records representing the > same probe. > However, the UCSC website record (shown below as record 1) > is completely > different from the original GNF website record (shown below > as record > 2). The two record values appear to be raw form. Looking at > this data, > the probe appears to be expressing in the UCSC record, > while it is not > in the GNF record. > > > > Can somebody explain why there is this discrepancy? > > > > 1. UCSC Table: > > clade: Mammal > > genome: Human > > assembly: Mar. 2006 > > group: Expression > > track: GNF Atlas 2 > > table: gnfHumanAtlas2All > > 208553_at 158 > 38,15,27,48,201,25,361,23,156,491,383,420,49,328,76,68,664,406,330,139,331,224,58,42,217,53,62,28,38,23,25,100,324,191,53,30,29,49,15,56,67,29,96,72,93,54,25,34,110,81,118,24,38,25,25,69,17,15,82,36,59,32,13,55,22,29,76,70,16,32,120,29,208,18,86,37,26,42,31,23,48,24,30,38,66,48,63,45,53,68,31,30,38,44,59,28,22,31,38,95,25,26,34,21,18,85,58,29,17,28,17,38,35,13,75,81,47,23,253,23,55,131,88,18,82,18,24,46,40,95,19,61,16,32,60,28,24,91,19,79,29,50,47,53,29,68,55,34,110,60,69,108,26,43,23,22,72,83, > > > > > > 2. From GNF (Novartis) site > > 208553_at 8.3 > 6.3 6.55 > 5.35 6.35 > 6.55 5.1 > 8.05 6.4 > 6.9 7.8 > 7.75 9.8 > 8.85 8.35 > 8 8.9 > 7.35 7.8 > 9.65 5.55 > 6.85 5 > 5.1 6.05 > 6.7 4.6 > 6.7 6.75 > 5.7 5.9 > 5.4 6.5 > 7.15 4.8 > 8.1 6.5 > 6.45 6.5 > 7.65 5.9 > 8.2 8.75 > 6.15 5.75 > 5.35 4.45 > 4.95 7 > 6.45 7.4 > 6.8 6.2 > 7.65 7.4 > 5.9 6.9 > 5.4 7.65 > 6.65 6.4 > 5.7 6.05 > 6.25 5.3 > 6.65 5.65 > 5.95 6.15 > 6.8 7.65 > 6.45 6.75 > 5.6 5.6 > 7.1 5.65 > 6.95 5.6 > > > > Thanks, > > > > Raj > > > > > > > _______________________________________________ > > Genome maillist - [email protected] > > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
