[BioC] [Fwd: Re: HTqPCR error]

[Heidi Dvinge]

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 Biología Celular y Molecular
> Facultad de Ciencias-Universidade da Coruña
> Tlf. +34 981 167000 ext 2030
> e-mail: jfernandezt at udc.es
> ----------------------------------------------------------------
>
>
>