[BioC] sir

[deepak roshan]

sir,

iam geting some error in reading raw data step. i converted all my realtime
pcr data into tad-delimited text file,along with that a text file listing
sample name
and biological condition,and one text file of SDS .With this mail iam
attaching that folder in which three text files are there 1- real time PCR
data which is named
as plate1 (like this 20 plate i have), 2- text file listing sample name and
biological condition,3- SDS file
this file was save in D drive and i changed the directory of R to the folder
HTqPCR.

out put of R work sheet i also attached with this mail whaen i give path to
read my data its reading the example data which is present the package.

thank you

Deepak





On 5/20/10, Heidi Dvinge <heidi at ebi.ac.uk> wrote:
>
> Dear Deepak,
>
> it should be possible to analyse this kind of data with HTqPCR. If you
> look through the manual (available at
> http://www.bioconductor.org/packages/devel/bioc/html/HTqPCR.html or by
> typing openVignette() in R), then in chapter 13 there should be some notes
> regarding how to handle multiple samples present on each individual plate.
> The rest of the manual goes through how to analyse qPCR data in general
> with HTqPCR, including examples of all the main commands.
>
> If you have any specific questions or problems along the way, then please
> just ask me (via the bioconductor email list,
> bioconductor at stat.math.ethz.ch). Remember to include some example code
> showing what you've done, and any error messages that might have occurred.
> This makes it easier for me and the other members of the BioConductor ist
> to help you.
>
> Best wishes
> \Heidi
>
> >  sir,
> >
> > thank for  your kind help. i tried as you said with R 2.11 and it is
> > working. i tried to analysis the example data with in that it worked
> well.
> > now i will try with my data, My data consist of 48 features represented
> > eight times on the array. using one TLDA card i have done 8 samples.
> > whether
> > this type of data can be analysed using HTqPCR.
> >
> > thanking you
> > deepak
> >
> >
> > try:
> >
> > source  ("http://www.bioconductor.org/biocLite.R")
> > biocLite("HTqPCR")
> >
> > Note the "www" - as your error message say, you don't actually source the
> > biocLite.R file, so you don't have an biocLite function, and therefore
> you
> > can't use biocLite to install anything.
> >
> > Regarding the version, I recommend you to use R-2.11 (the stable release
> > version) or perhaps R-2.12 (the development version) if you really need
> > some of the newer features for whatever reason. R-2.10 will give you
> > HTqPCR version 1.0.0, but it has changes quite a lot since then, so the
> > version 1.2.0 you get with R-2.11 is likely to be significantly easier to
> > use.
> >
> > \Heidi
> >
> >>
> >> > sir
> >> >
> >> > As asked for the output of session info when i used R 2.10.0 and R
> >> 2.12.0
> >> > along with that i have also added the output when i give        source
> >>  ("
> >> > http://bioconductor.org/biocLite.R")
> >> >                biocLite("HTqPCR")
> >> >
> >> > in R 2.10.0 and R 2.12.0. Please help solve the problem
> >> >
> >> > Thanking You
> >> >    Deepak
> >> >
> >> >
> >> >
> >> >
> >> > On 5/16/10, Heidi Dvinge <heidi at ebi.ac.uk> wrote:
> >> >>
> >> >> Dear Deepak,
> >> >>
> >> >> (cc'd to the bioconductor email list)
> >> >>
> >> >> > sir,
> >> >> >
> >> >> > Iam a PhD student working in cancer biology. Recently i have done
> >> >> > expression
> >> >> > analysis of 48 gene using TLDA. for the analysis of that that data
> >> i
> >> >> have
> >> >> > tried the R using
> >> >> > HTqPCR<http://www.ebi.ac.uk/bertone/software/HTqPCR_1.1.4.zip>in R
> >> >> > 2.11. but i give this
> >> >> > source  ("http://bioconductor.org/biocLite.R")
> >> >> >
> >> >> >
> >> >> >                        biocLite("HTqPCR")
> >> >> >
> >> >>
> >> >> Could you please provide the exact error you get when you try to use:
> >> >>
> >> >> source("http://bioconductor.org/biocLite.R")
> >> >> biocLite("HTqPCR")
> >> >>
> >> >> I'm afraid that without knowing the error message I can't know what
> >> the
> >> >> problem is. Also, please provide the output of:
> >> >>
> >> >> sessionInfo()
> >> >>
> >> >> so that we know what system + version you're on.
> >> >>
> >> >> On a side note, when you use biocLite, HTqPCR actually gets installed
> >> >> directly from the R repository, not from the URL you mention here
> >> >> (http://www.ebi.ac.uk/bertone/software/), but using biocLite is
> >> always
> >> >> the
> >> >> recommended way, since it will automatically get the package version
> >> >> compatible with your R/BioC installation, and all the required
> >> >> dependencies.
> >> >>
> >> >> HTH
> >> >> \Heidi
> >> >>
> >> >> >  to install the package of HTqPCR
> >> >> > <http://www.ebi.ac.uk/bertone/software/HTqPCR_1.1.4.zip> it shows
> >> that
> >> >> > some error is their i tried with different R versions but iam not
> >> able
> >> >> > to solve the problem. Could you please
> >> >> > help me solve me the problem with the analysis of real time PCR
> >> using
> >> >> > R with HTqPCR
> >> >> <http://www.ebi.ac.uk/bertone/software/HTqPCR_1.1.4.zip>.
> >> >> >
> >> >> >
> >> >> > thanking you
> >> >> >
> >> >> > --
> >> >> > Deepak Roshan V G
> >> >> > PhD student
> >> >> > Laboratory Of Cell Cycle Regulation  &   Molecular Oncology
> >> >> > Division of Cancer Research
> >> >> > Regional Cancer Centre
> >> >> > Thiruvananthapuram
> >> >> > Kerala, India 695 011
> >> >> >
> >> >>
> >> >>
> >> >>
> >> >
> >> >
> >> > --
> >> > Deepak Roshan V G
> >> > Laboratory Of Cell Cycle Regulation  &   Molecular Oncology
> >> > Division of Cancer Research
> >> > Regional Cancer Centre
> >> > Thiruvananthapuram
> >> > Kerala, India 695 011
> >> >
> >>
> >>
> >>
> >
> >
> > --
> > Deepak Roshan V G
> > Laboratory Of Cell Cycle Regulation  &   Molecular Oncology
> > Division of Cancer Research
> > Regional Cancer Centre
> > Thiruvananthapuram
> > Kerala, India 695 011
> >
>
>
>


-- 
Deepak Roshan V G
Laboratory Of Cell Cycle Regulation  &   Molecular Oncology
Division of Cancer Research
Regional Cancer Centre
Thiruvananthapuram
Kerala, India 695 011