Hello Patrick, sorry for the delay in replying. > Dear Heidi, > > I just found out about your R-package for analyzing PCR data. I started to > read about it but suffered with a silly problem. > My output files look like the ones attached: 1 per sample and 3 technical > replicate per file and used the following: > > files <- read.delim(file.path(path, "file listing.txt")) > raw <- readCtData(files=files$File, path=path, > n.features=48,feature=1,Ct=2,header=FALSE, SDS=FALSE) > > The readCtData command did not work. Could you give some assistance to a > non-frequent user of R? > In case this is still relevant, then the issue is that your file doesn't contain a lot of the standard high-throughput qPCR information, such as well position on a plate, and type of probe (control or 'real'). Therefore, you need to set these input to NULL. For examplke, this should work: > files <- read.delim("file listing.txt", as.is=TRUE) > raw <- readCtData(files=files$File, flag=NULL, feature=1, type=NULL, position=NULL, Ct=2, n.features=48) Warning message: In readCtData(files = files$File, flag = NULL, feature = 1, type = NULL, : One or more samples contain NAs. Consider replacing these with e.g. Ct=40 now. > show(raw) An object of class "qPCRset" Size: 48 features, 3 samples Feature types: Target Feature names: Hprt1 B2m Gapdh ... Feature classes: Feature categories: OK Sample names: 31H 34H 35H ... You can now continue as outlined in the vignette, and for example check the distribution of your Ct values: > plotCtBoxes(raw) > plotCtPairs(raw) Note the warning about missing values. You can keep those as NA if you prefer, but if you want to replace them you can say e.g. > exprs(raw)[is.na(exprs(raw))] <- 40 HTH \Heidi > Thank you so much. > > Best wishes, > > Patrick > > > Patrick De Boever, PhD, MSc > Flemish Institute for Technological Research (VITO) > Unit Environmental Risk and Health > Industriezone Vlasmeer 7, 2400 Mol, Belgium > Tel. + 32 14 33 51 45 > Fax. + 32 14 58 05 23 > patrick.deboever at vito.be<mailto:patrick.deboever at="" vito.be=""> > > Visit our website: www.vito.be/english<http: www.vito.be="" english=""> > > > > Uniting expertise from different fields of technology enhances the > development of innovative methods for sustainable production. > Join the third edition of the international congress 'Innovation for > Sustainable Production 2012' > May, 6-9, 2012 - Bruges (Belgium) > http://www.i-sup2012.org > --- > This e-mail, any attachments and the information it contains are > confidential and meant only for the use of the addressee(s) only. Access > to this e-mail by anyone other than the addressee(s) is unauthorized. If > you are not the intended addressee (or responsible for delivery of the > message to such person), you may not use, copy, distribute or deliver to > anyone this message (or any part of its contents) or take any action in > reliance on it. In such case, you should destroy this message and notify > the sender immediately. If you have received this e-mail in error, please > notify us immediately by e-mail or telephone and delete the e-mail from > any computer. > All reasonable precautions have been taken to ensure no viruses are > present in this e-mail and its attachments. As our company cannot accept > responsibility for any loss or damage arising from the use of this e-mail > or attachments we recommend that you subject these to your virus checking > procedures prior to use. > >