> 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="">

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=""> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

On 28 May 2010, at 16:01, deepak roshan wrote: > sir, > > I have 99 sample and they are tumor and normal but when i give > command to read the raw data it is reading only 6 sample and for > > show(raw) the out put is 6 samples. is this package is limited for > 6 sample if we can change the sample how it has to be done i tried > using > n.sample <- 99 ot was not working the detail of the session > in here... > You haven't actually read in any data in the example you provide below. data(qPCRraw) will load the qPCRset object called qPCRraw, which is an example dataset that comes with the HTqPCR package. head (read.delim(file.path(path, "files.txt"))) is simply included to show you what's in the "files.txt" file - note that you only /display/ the content, you don't actually assign it to anything in R as you would do with "<-", using e.g.: > file.info <- read.delim(file.path(path, "files.txt")) See the help pages ?head and ?read.delim if you're not sure about what the functions actually do. In order to read in your own data, you need the function readCtData (and the parameter n.data). Examples of how to use the function are provided in ?readCtData and the HTqPCR vignette. HTH \Heidi > How to change feature class this not my class, how change the > sample numbers,change name of gene > > > "n.samples <- 99" > [1] "n.samples <- 99" > > show(qPCRraw) > An object of class "qPCRset" > Size: 384 features, 6 samples > Feature types: Endogenous Control, Target > Feature names: Gene1 Gene2 Gene3 ... > Feature classes: Kinase, Marker, TF > Feature categories: OK, Undetermined > Sample names: sample1 sample2 sample3 ... > > > > > > "n.samples <- 99" > [1] "n.samples <- 99" > > data(qPCRraw) > > data(qPCRpros) > > class(qPCRraw) > [1] "qPCRset" > attr(,"package") > [1] ".GlobalEnv" > > head(read.delim(file.path(path, "files.txt"))) > File Treatment > 1 DC004.txt Tumor > 2 D289.txt Tumor > 3 N143A.txt Tumor > 4 N143C.txt Normal > 5 D330.txt Tumor > 6 D153.txt Tumor > > 99.samples > Error: unexpected symbol in "99.samples" > > n.sample<-99.sample > Error: unexpected symbol in "n.sample<-99.sample" > > n.samples <- 99 > > n.wells <- 48 > > head(read.delim(file.path(path, "files.txt"))) > File Treatment > 1 DC004.txt Tumor > 2 D289.txt Tumor > 3 N143A.txt Tumor > 4 N143C.txt Normal > 5 D330.txt Tumor > 6 D153.txt Tumor > > data(qPCRraw) > > data(qPCRpros) > > class(qPCRraw) > [1] "qPCRset" > attr(,"package") > [1] ".GlobalEnv" > > show(qPCRraw) > An object of class "qPCRset" > Size: 384 features, 6 samples > Feature types: Endogenous Control, Target > Feature names: Gene1 Gene2 Gene3 ... > Feature classes: Kinase, Marker, TF > Feature categories: OK, Undetermined > Sample names: sample1 sample2 sample3 ... > > sessionInfo() > R version 2.11.0 (2010-04-22) > i386-pc-mingw32 > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > attached base packages: > [1] stats graphics grDevices utils datasets methods base > other attached packages: > [1] HTqPCR_1.2.0 limma_3.4.0 RColorBrewer_1.0-2 > Biobase_2.8.0 > loaded via a namespace (and not attached): > [1] affy_1.26.1 affyio_1.16.0 gdata_2.8.0 > [4] gplots_2.7.4 gtools_2.6.2 preprocessCore_1.10.0 > [7] tools_2.11.0 > > > Thanking you > > > > > -- > Deepak Roshan V G > Laboratory Of Cell Cycle Regulation & Molecular Oncology > Division of Cancer Research > Regional Cancer Centre > Thiruvananthapuram > Kerala, India 695 011

> > Dear sir, > > thank you for your all help. iam facing some problems in raedCtData > step. i have 99 sample but it is deading only 6 samples.how the > sample numbers can be incereased to 99. details of the session is > given below > > deepak > > > n.samples <- 99 > > readCtData(files = files$File, path = path, n.features = 48, flag > = 4, feature = 6, type = 7, position = 3, Ct = 8, header = FALSE, > SDS = FALSE, n.data = 1, samples, na.value = 40) > An object of class "qPCRset" > Size: 48 features, 6 samples > Feature types: Endogenous Control, Target > Feature names: CCNF-Hs00171049_m1 RBL2-Hs00180562_m1 > CCND1-Hs00277039_m1 ... > Feature classes: > Feature categories: OK > Sample names: Sample1 Sample2 Sample3 ... > Warning message: > In readCtData(files = files$File, path = path, n.features = 48, : > Not enough sample names provided; using Sample1, Sample2, ... > instead > Hello Deepak, there is nothing in readCtData specifying that only 6 samples can be read. Defining a variable n.samples isn't going to change that, since you don't actually use this variable anywhere. What matters here is if your length(files$File) is 99. What does just: > files$File say? In the example data there are only 6 files, but if I read some of them multiple times, I can say: > exPath <- system.file("exData", package="HTqPCR") > exFiles <- read.delim(file.path(exPath, "files.txt")) > raw <- readCtData(files=exFiles$File[c(1:6,2:5,1:6)], path=exPath) > raw An object of class "qPCRset" Size: 384 features, 16 samples Feature types: Endogenous Control, Target Feature names: Gene1 Gene2 Gene3 ... Feature classes: Feature categories: OK, Undetermined Sample names: sample1 sample2 sample3 ... However, note that you do get a warning message about sample names. In your readCtData command, you include "samples". This is meant to be a character vector of sample names, if you don't want to use file names as sample names. Have you actually defined a variable called "samples" anywhere?? If you have your sample names in e.g. a vector called my.samplenames, then you need to run readCtData with: readCtData(files = files$File, path = path, n.features = 48, flag = 4, feature = 6, type = 7, position = 3, Ct = 8, header = FALSE, SDS = FALSE, n.data = 1, samples=my.samplenames, na.value = 40) If not, then skip the "samples" parameter altogether and say: readCtData(files = files$File, path = path, n.features = 48, flag = 4, feature = 6, type = 7, position = 3, Ct = 8, header = FALSE, SDS = FALSE, n.data = 1, na.value = 40) Does that change anything? \Heidi > > head(read.delim(file.path(path, "files.txt"))) > File Treatment > 1 Sample4.txt Tumor > 2 Sample67.txt Tumor > 3 Sample80.txt Tumor > 4 Sample44.txt Tumor > 5 Sample76.txt Tumor > 6 Sample94.txt Normal > > tail(read.delim(file.path(path, "files.txt"))) > File Treatment > 94 Sample37.txt Tumor > 95 Sample32.txt Tumor > 96 Sample33.txt Tumor > 97 Sample34.txt Tumor > 98 Sample25.txt Tumor > 99 Sample26.txt Normal > > > sessionInfo() > R version 2.11.0 (2010-04-22) > i386-pc-mingw32 > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C LC_TIME=English_United > States.1252 > attached base packages: > [1] stats graphics grDevices utils datasets methods base > other attached packages: > [1] HTqPCR_1.2.0 limma_3.4.0 RColorBrewer_1.0-2 > Biobase_2.8.0 > loaded via a namespace (and not attached): > [1] affy_1.26.1 affyio_1.16.0 > gdata_2.8.0 gplots_2.7.4 gtools_2.6.2 > preprocessCore_1.10.0 > [7] tools_2.11.0 > > [[alternative HTML version deleted]]