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Heidi Dvinge ★ 2.0k
@heidi-dvinge-2195
Last seen 9.6 years ago
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 >
Cancer cycle HTqPCR Cancer cycle HTqPCR • 986 views
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@deepak-roshan-4103
Last seen 9.6 years ago
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
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