[BioC] Reading in data with HTqPCR
Heidi Dvinge
heidi at ebi.ac.uk
Thu May 27 15:26:18 CEST 2010
> 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
>
Hello Deepak,
first, a few comments. Attachments aren't accepted to the
BioConductor list and are stripped. Therefore, please always provide
the code you used and the error messages you got in the actual email.
Also, always include the output of sessionInfo(), so people on the
list can see whether the error you get is related to your R an/or
package version.
The commands you include in your file are:
> all.R.commands <- system.file("doc", "HTqPCR.Rnw", package =
"HTqPCR")
> Stangle(all.R.commands)
Writing to file HTqPCR.R
> ls("package:HTqPCR")
Error in as.environment(pos) :
no item called "package:HTqPCR" on the search list
Don't forget that every time you want to use a package, you have to
load it with library(). Just having it installed in R is not
sufficient, so in you case you need library(HTqPCR).
> path <- d:\("HTqPCR\tlda", package="HTqPCR")
Error: unexpected input in "path <- d:\"
This gives an error, so you haven't actually changed the path! This
is why it still reads in the default data. Also, unless you've
actually put your data in the folder where HTqPCR is installed from
(bad idea), you just need the path itself. You have your d:\ outside
the quotes, so you'll need something like:
path <- "d:\HTqPCR\tlda"
In general, warnings messages are just for your information, but when
you get an error message from a command you tried to run, this means
it didn't work! Just continuing as if nothing happened is bound to
make things fail further down the line, or give you unwanted results.
HTH
\Heidi
>
>
>
>
> 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 <HTqPCR.rar><R version 2.doc>
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