[BioC] HTqPCR error

[Heidi Dvinge]

> 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 Biología Celular y Molecular
> Facultad de Ciencias-Universidade da Coruña
> Tlf. +34 981 167000 ext 2030
> e-mail: jfernandezt at udc.es
> ----------------------------------------------------------------
>
>
>
> De: "Heidi Dvinge" <heidi at ebi.ac.uk>
> Para: "\"Juan Fernández 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 Biología Celular y Molecular
>> Facultad de Ciencias-Universidade da Coruña
>> Tlf. +34 981 167000 ext 2030
>> e-mail: jfernandezt at udc.es
>> ----------------------------------------------------------------
>>
>>
>>
>
>
>