[BioC] Reading in data with HTqPCR
James W. MacDonald
jmacdon at med.umich.edu
Thu May 27 16:35:04 CEST 2010
One additional point about paths (see below)
Heidi Dvinge wrote:
>> 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"
This won't work as a path, as the '\' is used in R as an escape
> path <- "d:\HTqPCR\tlda"
Error: '\H' is an unrecognized escape in character string starting "d:\H"
so you have to either double up:
path <- "d:\\HTqPCR\\tlda"
or IMO, preferably, use Unix path separators
path <- "d:/HTqPCR/tlda"
Best,
Jim
>
> 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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--
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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