> Dear Heidi, > > After trying the two combinations that you talked about, just the second > one worked, i.e: > > raw1 <- readCtData(files="Prueba_Blanco001.txt", n.features=96, n.data=96, > column.info=list(flag=9, feature=5, type=6, Ct=7, position=1), skip=12, > sep="\t") > > the first one, gave the same previous error. > >> temp <- readCtData(files="Prueba_Blanco001.txt", n.features=96*96, > + format="BioMark") > Error en `$<-.data.frame`(`*tmp*`, "Call", value = character(0)) : > replacement has 0 rows, data has 9216 > Okay, so it looks like the order and/or column names in your file is different from the Fluidigm files the readCtData is based on, and the n.features/n.data parameters are working as they should (phew). Could you perhaps send me the header of your file, so I can see what the different is? \Heidi > Thanks > > Juan > > > > --------------------------------------------------------------- > Juan Fernandez Tajes, ph. D > Grupo XENOMAR > Departamento de Biolog?a Celular y Molecular > Facultad de Ciencias-Universidade da Coru?a > Tlf. +34 981 167000 ext 2030 > e-mail: jfernandezt at udc.es > ---------------------------------------------------------------- > > > > De: "Heidi Dvinge" <heidi at="" ebi.ac.uk=""> > Para: "\"Juan Fern?ndez Tajes\"" <jfernandezt at="" udc.es=""> > Enviados: Jueves, 13 de Septiembre 2012 2:56:43 > Asunto: Re: HTqPCR error > > Hi Juan, > >> Dear Heidi, >> >> My name is Juan Fernandez-Tajes and I?m using HTqPCR for analyzing some >> Biomark 96*96 data. When I tried the following command I got an error: >> >>>raw1 <- readCtData(files="Prueba_Blanco001.txt", format="BioMark", >>> n.features=96, n.data=96) >> Error en `$<-.data.frame`(`*tmp*`, "Call", value = character(0)) : >> replacement has 0 rows, data has 9216 >> >> However when I import the data with the following command it works: >> >>>temp <- readCtData(files="Prueba_Blanco001.txt", n.features=96*96, >>> column.info=list(flag=9, feature=5, type=6, Ct=7, position=1), skip=12, >>> sep="\t") >>>raw <- changeCtLayout(temp, sample.order=rep(1:96, each=96)) >> >> Any ideas? >> > Not at the top of my head. However, you actually change two things here, > namely both the specification of n.features/n.data and using 'format' vs > 'column.info'. To help me figure out which of these two things causes the > error, can you try running the remaining 2 combinations? I.e.: > > temp <- readCtData(files="Prueba_Blanco001.txt", n.features=96*96, > format="BioMark") > > raw1 <- readCtData(files="Prueba_Blanco001.txt", n.features=96, n.data=96, > column.info=list(flag=9, feature=5, type=6, Ct=7, position=1), skip=12, > sep="\t") > > Thanks > \Heidi > >> Many thanks in advance >> >> Juan >> >> --------------------------------------------------------------- >> Juan Fernandez Tajes, ph. D >> Grupo XENOMAR >> Departamento de Biolog?a Celular y Molecular >> Facultad de Ciencias-Universidade da Coru?a >> Tlf. +34 981 167000 ext 2030 >> e-mail: jfernandezt at udc.es >> ---------------------------------------------------------------- >> >> >> > > >