ate: Mon, 01 Sep 2008 22:47:29 -0400 From: Alfred Hero To: Tim Veldman CC: Aimee Zaas , "Alfred O. Hero" , Brett Caram , Carolyn Talcott , Christine Oien , Christopher W Woods , Geoff Ginsburg , Jay B Varkey , Lawrence Carin , Patrick Lincoln , Rita L Chambers , Sara Hoffman , Stephen Kingsmore , "'Eley, Greg [USA]'" Subject: Re: Reminder: Duke PHD Project Team Meeting 9/2 1130AM Dear Team - the normalization of the RSV data is complete and the data has been uploaded to the server in a folder called RSV-GEP. There you will find5 files 1) darpa.rsv.rma.(164).ccdf.txt RMA preprocessed singal intensity for complete set of 164 gene expression profiles. 2) residual.plots.zip Archive file including all the residual plots for visual examination. 3) darpa.rsv.rma.(164).residual.ppt Slides showing chips with minor to mild artifacts. 4) darpa.rsv.key.txt Key mapping chips, samples and subjects. 5) readme.txt Look forward to talking with you all on the phone call tomorrow. Al ============================================================================== Date: Tue, 02 Sep 2008 23:06:47 -0400 From: Alfred Hero To: Tim Veldman CC: Aimee Zaas , "Alfred O. Hero" , Brett Caram , Carolyn Talcott , Christine Oien , Christopher W Woods , Geoff Ginsburg , Jay B Varkey , Lawrence Carin , Patrick Lincoln , Rita L Chambers , Sara Hoffman , Stephen Kingsmore , "'Eley, Greg [USA]'" Subject: Re: Reminder: Duke PHD Project Team Meeting 9/2 1130AM Team - the data that we uploaded yesterday was not log2 transformed and that is why the values were of different order of magnitude from the Rhino data. For those analysts who wish to not perform this transform themselves you can download the log2 transformed data from the website. Otherwise you simply need to apply the log2 operator to the matrix that you downloaded previously. Thanks Carolyn for catching this and sorry for the confusion. Al ============================================================================== Date: Thu, 04 Sep 2008 10:01:54 -0400 From: Alfred Hero To: Patrick Lincoln , Lawrence Carin Subject: [Fwd: Urgent update on the key i sent to you (subject #8)] Pat and Larry - due to some ambiguity on Duke's key the phenotype for subject 008 in the RSV key file is wrong. It should be changed to Asx. regards Al -------- Original Message -------- Subject: Urgent update on the key i sent to you (subject #8) Date: Wed, 3 Sep 2008 21:10:42 -0400 From: Yongsheng To: 'Alfred Hero' prof hero, in the key sent to us from Duke, there is a slight descrepancy on subject #8 wrt its class label. from the top panel it says "YES" for #8. (AND THAT"S WHAT I GAVE TO YOU AS WELL). However, at the bottom panel, #8 becomes Asx. By looking at the symtom score, it seems to me #8 is Asx. That means the key i gave to you is WRONG. You change all #8 into Asx. Sorry about this. I did not see it when i generate the key. yongsheng ============================================================================== Date: Thu, 04 Sep 2008 18:18:52 -0400 From: Alfred Hero To: clt@csl.sri.com CC: huangys@umich.edu, pdl@csl.sri.com, Christine Oien , Aimee Zaas , Tim Veldman Subject: Re: Urgent update on the key i sent to you (subject #8) Carolyn - We did get the shedding classification on Rhino data but I have not seen it for the RSV data. I agree that this would be useful but, as far as I understand, shedding does not have anything to do with the asx and sx classification (indeed in rhino there were some shedding submjects classified as asx and vice versa). We had nothing to do with these asx and sx classifications. I am copying Christine and Aimee on this to see if they can provide additional information. Al Carolyn Talcott wrote: > Would it be possible to get the original data from which the > Asx / Sx classification was made? Is the shedding/sero conversion > data available / part of the classification input? > > Thanks, > Carolyn >