Re: [R] filtering a dataframe with a vector of rownames
subset(data, row.names(data) %in% name.to.keep HTH, Anjan On Fri, Jan 14, 2011 at 1:25 PM, Jonathan Hughes jonathan.hughes...@live.com wrote: Hello, Here's my problem. I have a large data frame and a vector with some of its row names. I'd like to have a new data frame only with those rows that match this vector of row names. I tried this: data-cbind(c(1,2,3,4,5,6),c(2,3,4,5,6,7)) rownames(data)-c(a, b, c,d,e,f) names.to.keep-c(a, c, d) rows.to.keep-which(rownames(data)==names.to.keep) But it didn't work. Any suggestions? thanks a lot. Jonathan. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- === anjan purkayastha, phd. research associate fas center for systems biology, harvard university 52 oxford street cambridge ma 02138 phone-703.740.6939 === [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Plotting colour-coded points
Hi, I have a file of the following type: idab 1 0.5 5 2 0.7 15 3 1.6 7 40.5 25 I would like to plot the data in column a on the y-axis and the corresponding data in column id on the x-axis, so plot(a~id). However I would like to colour these points according to the data in column b. column b data may be colour coded into the following bins: 0-9; 10-19; 20-29. Any idea on how to accomplish this? TIA, Anjan -- === anjan purkayastha, phd. research associate fas center for systems biology, harvard university 52 oxford street cambridge ma 02138 phone-703.740.6939 === [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] subset question
Hi, I'm having a problem with a step that should be pretty simple. I have a dataframe, d, with column names : gene s1 s2 s3. The column gene stores an Id; the rest of the columns store intensity data. I would like to extract the rows for gene Ids i1, i2, i3 ( I know a priori that those rows exist). So I do this: subset(d, gene %in% c(i1, i2, i3)). This does not give me the required data. Any ideas where I am going wrong? TIA, Anjan -- === anjan purkayastha, phd. research associate fas center for systems biology, harvard university 52 oxford street cambridge ma 02138 phone-703.740.6939 === [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] subset question
nope, that did not work. thanks though. Anjan On Wed, Dec 29, 2010 at 5:02 PM, Jonathan Flowers jonathanmflow...@gmail.com wrote: Try subd - d[, gene == c(i1,i2,i3)] On Wed, Dec 29, 2010 at 4:55 PM, ANJAN PURKAYASTHA anjan.purkayas...@gmail.com wrote: Hi, I'm having a problem with a step that should be pretty simple. I have a dataframe, d, with column names : gene s1 s2 s3. The column gene stores an Id; the rest of the columns store intensity data. I would like to extract the rows for gene Ids i1, i2, i3 ( I know a priori that those rows exist). So I do this: subset(d, gene %in% c(i1, i2, i3)). This does not give me the required data. Any ideas where I am going wrong? TIA, Anjan -- === anjan purkayastha, phd. research associate fas center for systems biology, harvard university 52 oxford street cambridge ma 02138 phone-703.740.6939 === [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- === anjan purkayastha, phd. research associate fas center for systems biology, harvard university 52 oxford street cambridge ma 02138 phone-703.740.6939 === [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Error message when creating a dataframe
Hi, I'm creating a data frame of 24 columns and 45101 rows. Here is the error I get: R(147,0xa04d8720) malloc: *** mmap(size=184320) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Any idea of what I can do to trouble-shoot? Attached is the session info: R version 2.11.1 (2010-05-31) i386-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base Thanks in advance, Anjan -- === anjan purkayastha, phd. research associate fas center for systems biology, harvard university 52 oxford street cambridge ma 02138 phone-703.740.6939 === [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] One-class SVM
Does any R package support one-class SVM? I'm trying to develop an application to detect anomalies in genome sequencing. Thanks in advance. Anjan -- === anjan purkayastha, phd. research associate fas center for systems biology, harvard university 52 oxford street cambridge ma 02138 phone-703.740.6939 === [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Subsetting a dataframe
Hi, I have a dataframe with 43 columns and a 1000 rows. Each entry in the dataframe can be either P or A. here is a small chunk: c1c2 ...c43 r100 P A ... P r101 A A ... A r102 P P ... P How does one subset this data frame to select those rows that have only P's in them? Thanks in advance. Anjan -- === anjan purkayastha, phd. research associate fas center for systems biology, harvard university 52 oxford street cambridge ma 02138 phone-703.740.6939 === [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Subsetting a dataframe
Thanks all for your help. Anjan On Sun, Oct 24, 2010 at 1:38 PM, Jorge Ivan Velez jorgeivanve...@gmail.comwrote: Hi Anjan, Please consider the following example: x - c(2, rep(1, 10)) all(x == 1) [1] FALSE d - replicate(10, sample(x, replace = TRUE)) d [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [1,]111111211 1 [2,]111212121 1 [3,]111111111 1 [4,]111111112 1 [5,]111121111 1 [6,]211111111 1 [7,]111111112 1 [8,]112111111 1 [9,]122121112 1 [10,]111111111 1 [11,]111111111 1 d[apply(d, 1, function(v) all(v==1)), ] [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [1,]111111111 1 [2,]111111111 1 [3,]111111111 1 HTH, Jorge On Sun, Oct 24, 2010 at 1:32 PM, ANJAN PURKAYASTHA wrote: Hi, I have a dataframe with 43 columns and a 1000 rows. Each entry in the dataframe can be either P or A. here is a small chunk: c1c2 ...c43 r100 P A ... P r101 A A ... A r102 P P ... P How does one subset this data frame to select those rows that have only P's in them? Thanks in advance. Anjan -- === anjan purkayastha, phd. research associate fas center for systems biology, harvard university 52 oxford street cambridge ma 02138 phone-703.740.6939 === [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- === anjan purkayastha, phd. research associate fas center for systems biology, harvard university 52 oxford street cambridge ma 02138 phone-703.740.6939 === [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How do I tell whether two vectors are identical?
Hi, I have two vectors, each of length 45000. How do I compare the vectors to ascertain if they are identical. Secondly if they are NOT identical, how do I determine the indices of positions at which the vectors differ? Thanks, Anjan -- === anjan purkayastha, phd. research associate fas center for systems biology, harvard university 52 oxford street cambridge ma 02138 phone-703.740.6939 === [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How do I tell whether two vectors are identical?
Thanks all for you help. Anjan 2010/10/12 £ukasz Rêc³awowicz lukasz.reclawow...@gmail.com Or just: id-seq(1,45e3,1) compare-data.frame(id,a,b) differences-compare$id[a!=b] -- Mi³ego dnia __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- === anjan purkayastha, phd. research associate fas center for systems biology, harvard university 52 oxford street cambridge ma 02138 phone-703.740.6939 === [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] problem with colors
Hi Phil and Thomas, Thanks for your helpful feedback. I must admit my solution to creating the vector of colors lacked your elegance. In brief, I saved the output of colors() into a text file, saved all but 47 colours in that file and read it back as a data frame and used the first column of the dataframe as a vector of 47 colours. This roundabout method may have caused the problem because when I chose colours according to the commands sent by both of you things seemed to work just fine. Thank you very much for your feedback. Anjan On Thu, Oct 7, 2010 at 3:25 PM, Thomas Stewart tgstew...@gmail.com wrote: I would be helpful if you provided a more complete, reproducible example. Consider the following code. It colors the boxes according to the first 47 colors listed in the color() vector. -tgs data-as.data.frame(matrix(rnorm(47*23),ncol=47)) boxplot(data,col=colors()[1:47]) On Thu, Oct 7, 2010 at 2:22 PM, ANJAN PURKAYASTHA anjan.purkayas...@gmail.com wrote: Hi, I have a data set of 47 columns. I would like to create a boxplot for each column, each boxplot of a different colour. So I created a vector col1. This vector has a subset of the colors returned by color()- red, cyan, green etc. Now I use the command: boxplot(dataset, col= col1) expecting to see 47 boxplots, each of a different colour. Here is the problem: the boxplots are drawn correctly but it seems that only the first few colours in col1 are being used in a repeated pattern. Anybody has any ideas on how to tackle this? Thanks in advance, Anjan -- === anjan purkayastha, phd. research associate fas center for systems biology, harvard university 52 oxford street cambridge ma 02138 phone-703.740.6939 === [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- === anjan purkayastha, phd. research associate fas center for systems biology, harvard university 52 oxford street cambridge ma 02138 phone-703.740.6939 === [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] problem with colors
Hi, I have a data set of 47 columns. I would like to create a boxplot for each column, each boxplot of a different colour. So I created a vector col1. This vector has a subset of the colors returned by color()- red, cyan, green etc. Now I use the command: boxplot(dataset, col= col1) expecting to see 47 boxplots, each of a different colour. Here is the problem: the boxplots are drawn correctly but it seems that only the first few colours in col1 are being used in a repeated pattern. Anybody has any ideas on how to tackle this? Thanks in advance, Anjan -- === anjan purkayastha, phd. research associate fas center for systems biology, harvard university 52 oxford street cambridge ma 02138 phone-703.740.6939 === [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Plotting x-axis labels perpendicular to the axis
Hi, The following command: axis(1, at= 1:50, labels= sampleNames(data)) produces an X-axis with 50 ticks and labels drawn from the sampleNames namespace. Problem is the labels at each tick are printed parallel to the x-axis and thus run into each other. How do I specify for the labels to be printed perpendicular to the x-axis? Thanks in advance. Anjan -- === anjan purkayastha, phd. research associate fas center for systems biology, harvard university 52 oxford street cambridge ma 02138 phone-703.740.6939 === [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] subsetting
Hi, I have a data-frame, r (column names below), that needs subsetting: date, time, strain, gene, deltact When I try to subset r by applying selection criteria on two columns I get an empty data frame. For example I would like to extract all rows that have time == 0h and strain == ROC. So, t - subset(r, (r$time == 0h r$strain == ROC), select= c(time, strain, gene, deltact)) returns an empty data-frame. Is it not possible to subset based on two criteria? TIA Anjan -- === anjan purkayastha, phd. research associate fas center for systems biology, harvard university 52 oxford street cambridge ma phone-703.740.6939 === [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] modifying only certain rows in a data-frame
Hi, I have a data-frame r (shown below is a subset) with the following column names: datetimesamplevctnormhctdeltact $time has 8 levels: 0h, 0.5h, .24h. $deltact holds real numbers. I want to subset this dataframe by the levels of $time. For all the rows which have r$time == 0h I would like to convert the present value of r$deltact to 0. Any pointers to a simple method to accomplish would be greatly appreciated. TIA, Anjan -- === anjan purkayastha, phd. research associate fas center for systems biology, harvard university 52 oxford street cambridge ma phone-703.740.6939 === [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] plotting the following data
Hi, I need to plot $time on the x-axis and $f on the y-axis for the following data: timef 0h0.00 0.5h0.54 1h1.15 2h2.33 4h1.57 6h2.19 18h1.45 24h1.79 I want the order of the data-points to be retained and the x-coordinates of each of the 8 data-points to be equally spaced. however, using plot($time, $f) completely scrambles the ordering of the points. Any pointers to this newbie on how to plot these data points accurately will be much appreciated. Thanks, Anjan [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plotting the following data
Thanks all for your suggestions. plot(1:8, f, axes=FALSE) axis(1, at=1:8, labels=time) axis(2) That gave me exactly what I wanted. Anjan On Fri, May 21, 2010 at 12:27 PM, jim holtman jholt...@gmail.com wrote: Not exactly sure what you mean by equally spaced; here is one way: x - read.table(textConnection(timef + 0h0.00 + 0.5h0.54 + 1h1.15 + 2h2.33 + 4h1.57 + 6h2.19 + 18h1.45 + 24h1.79), header=TRUE, as.is=TRUE) plot(x$f, xaxt='n') axis(1, at=1:8, labels=x$time) On Fri, May 21, 2010 at 12:15 PM, ANJAN PURKAYASTHA anjan.purkayas...@gmail.com wrote: Hi, I need to plot $time on the x-axis and $f on the y-axis for the following data: timef 0h0.00 0.5h0.54 1h1.15 2h2.33 4h1.57 6h2.19 18h1.45 24h1.79 I want the order of the data-points to be retained and the x-coordinates of each of the 8 data-points to be equally spaced. however, using plot($time, $f) completely scrambles the ordering of the points. Any pointers to this newbie on how to plot these data points accurately will be much appreciated. Thanks, Anjan [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] row-wise means
I have a dataframe with 3 columns. The first column stores an index. I would like to calculate the mean of the numbers stored in each of the rest of the columns. So, here is my data matrix: col1 col2 col3 1 23 34 2 45 56 3 23 56 4 34 68 For each row I would like to calculate the means of the numbers stored in col2 and col3. How can this be done in R? TIA, Anjan -- = anjan purkayastha, phd bioinformatics analyst whitehead institute for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Filtering on a dataframe- newbie question
Thank you all who replied to my post. That cleared things up very well Anjan On Sun, Oct 18, 2009 at 11:10 PM, ANJAN PURKAYASTHA anjan.purkayas...@gmail.com wrote: Hi, newbie question. I have a data-frame with 3 named columns: Name, Obs1, Obs2. The Name column members are made of alphanumeric characters: T1, T2, T3 etc. I would like to acess only that subset of the data-frame with Name == T44. X - dataframe[dataframe$Name=='T44'] does not work. Any ideas on how to do this? I'm sure I'm missing a simple concept here. Thanks, Anjan -- = anjan purkayastha, phd bioinformatics analyst whitehead institute for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939 -- = anjan purkayastha, phd bioinformatics analyst whitehead institute for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Filtering on a dataframe- newbie question
Hi, newbie question. I have a data-frame with 3 named columns: Name, Obs1, Obs2. The Name column members are made of alphanumeric characters: T1, T2, T3 etc. I would like to acess only that subset of the data-frame with Name == T44. X - dataframe[dataframe$Name=='T44'] does not work. Any ideas on how to do this? I'm sure I'm missing a simple concept here. Thanks, Anjan -- = anjan purkayastha, phd bioinformatics analyst whitehead institute for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Calculating the average after adding 3 matrices
Hi all, Here is my problem: I have 3 matrices , A, B, C. Each is an nXn matrix. I need to create matrix D such that : D[i,j]= (A[i,j]+B[i,j]+C[i,j])/3. Being a newbie this is proving to be a challenge. Any ideas on how best to accomplish this? Thanks! Anjan -- = anjan purkayastha, phd bioinformatics analyst whitehead institute for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Book on R programming
Most books on R I come across describe running statistical procedures in R. Any suggestions on a good book that teaches *programming* in R? Thanks, Anjan -- = anjan purkayastha, phd bioinformatics analyst whitehead institute for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Book on R programming
To All, Your prompt and helpful replies are most appreciated. I'll be sure to check out your suggestions. Cheers, Anjan On Mon, Aug 31, 2009 at 8:24 AM, Ottorino-Luca Pantani ottorino-luca.pant...@unifi.it wrote: ANJAN PURKAYASTHA ha scritto: Most books on R I come across describe running statistical procedures in R. Any suggestions on a good book that teaches *programming* in R? Thanks, Anjan Here there are a few http://www.r-project.org/doc/bib/R-books.html [42] and [79] may be good starting points -- Ottorino -- = anjan purkayastha, phd bioinformatics analyst whitehead institute for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Plotting question
Hi I have a data set that needs to be plotted (see below) When I plot it using the simple plot(read_count ~ Cn), I get box plots for the read_count numbers plotted according to Cn. The Cn's on the x-axis are ordered: 1, 100, 1000, 40, 400, 4000... How do I plot so that Cn is plotted on the x-axis in an ascending order: 40, 60, 80, ...1? Thanks for your help. Anjan ID Cn read_count 1 MJ-2000-79 10,000 6876 2 MJ-2000-80 10,000 23440 3 MJ-2000-87 10,000 18787 4 MJ-2000-100 8000 4775 5 MJ-2000-81 8000 1542 6 MJ-2000-82 8000 1550 7 MJ-2000-101 6000 15322 8 MJ-2000-83 6000 7023 9 MJ-2000-84 6000834 10 MJ-2000-102 4000 4216 11 MJ-2000-85 4000 1174 12 MJ-2000-86 4000404 13 MJ-4000-131 1000 1368 14 MJ-4000-132 1000 2219 15 MJ-4000-125800413 16 MJ-4000-133800 2594 17 MJ-4000-127600 3059 18 MJ-4000-134600 1561 19 MJ-4000-142600848 20 MJ-4000-129400182 21 MJ-4000-130400 1410 22 MJ-4000-135400 2713 23 MJ-7000-182100943 24 MJ-8000-184100318 25 MJ-8000-185 80 92 26 MJ-8000-186 80161 27 MJ-8000-188 60158 28 MJ-8000-191 60103 29 MJ-8000-192 40468 30 MJ-8000-193 40432 -- = anjan purkayastha, phd bioinformatics analyst whitehead institute for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] drawing a plot with SEM
I have a data matrix: repeat1repeat2 13034 21223 3 50 13 4 5698 . . . I would like to plot for the mean and standard error of mean of repeat 1 and repeat2 for each row. Any pointers on how to do this in R? TIA, Anjan -- = anjan purkayastha, phd bioinformatics analyst whitehead institute for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Uninstall question
I need to uninstall R 2.7.1 from my Mac. What is the best way to uninstall it? Simply delete the R icon in the Applications folder? Or is it more involved? TIA, Anjan -- = anjan purkayastha, phd bioinformatics analyst whitehead institute for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] question on statistical test
hi, this is more of a statistical methodology question than an R question. however, since there are quite a few expert statisticians in this forum i think i can expect to get some useful feedback. here is my problem: i am studying a set of genes. for each gene i have a set of probes (there are 2-5 probes per gene). for each probe i have a set of 3 measurements (under conditions a, b and c). let us say that for a given gene i have 3 probes X, Y and Z. and for each probe there are 3 measurements, thus: a b c X Xa Xb Xc Y Ya YbYc ZZa ZbZc for each gene i need to test the correlation among the measurements under each condition. so, are Xa, Ya, Za correlated AND Xb, Yb, Zb correlated AND Xc, Yc, Zc correlated? based on the degree of correlation among these probe measurements i will choose the genes for further study. of course i have to do this for each gene in my set of 100. what statistical tests do i need to perform to accomplish this? all advice will be appreciated. tia, anjan [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] quantile question
Hi, A simple quantile question: I need to calculate the 95% and 5% quantiles (aka percentiles) for the following data: 67.12 64.51 62.06 55.45 51.41 43.78 10.74 10.14 if I use the formula: 95% quantile point= 95 (8+1)/100, I get the 8.55th point as the 95% quantile. Which does not make too much sense as I have only 8 data points. The other option is to use (95*8)/100 = 7.6th data point (which can be found by interpolation between the 7th and 8th data points). Reportedly, the second formula is not too accurate. However in my case the first formula does not make much sense. Any advice? TIA, Anjan -- = anjan purkayastha, phd bioinformatics analyst whitehead institute for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] quantile question
Thanks all for your prompt and helpful replies! Anjan On Thu, Jan 22, 2009 at 11:52 AM, ANJAN PURKAYASTHA anjan.purkayas...@gmail.com wrote: Hi, A simple quantile question: I need to calculate the 95% and 5% quantiles (aka percentiles) for the following data: 67.12 64.51 62.06 55.45 51.41 43.78 10.74 10.14 if I use the formula: 95% quantile point= 95 (8+1)/100, I get the 8.55th point as the 95% quantile. Which does not make too much sense as I have only 8 data points. The other option is to use (95*8)/100 = 7.6th data point (which can be found by interpolation between the 7th and 8th data points). Reportedly, the second formula is not too accurate. However in my case the first formula does not make much sense. Any advice? TIA, Anjan -- = anjan purkayastha, phd bioinformatics analyst whitehead institute for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939 -- = anjan purkayastha, phd bioinformatics analyst whitehead institute for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Perl-R bridge
Hi, I'm planning to access R from my perl scripts. The only noteworthy bridge seems to be Statistics-R-0.03http://search.cpan.org/%7Ectbrown/Statistics-R/lib/Statistics/R.pm. Would anyone like to share their experience with this Perl-R bridge? I'd like to install it in a Mac OS X. Suggestions on alternate solutions will be appreciated. Thanks in advance, Anjan -- = anjan purkayastha, phd bioinformatics analyst whitehead institute for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Statistics forums
Hi, Given that the R forum is mostly a site to discuss issues related to the language, are there any forums that discuss statistical issues? I am specifically interested in the statistical issues in experimental design. TIA, Anjan -- = anjan purkayastha, phd bioinformatics analyst whitehead institute for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] package question
hi, am new to R. what command do i use to check of certain packages have been loaded? Also, it seems that most packages come with vignette- is this a document that describes the usage of the package? thanks for your help, anjan -- = anjan purkayastha, phd bioinformatics analyst whitehead institute for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] printing all rows
Hi, my data table has 38939 rows. R prints the first 1 columns and then prints an error message:[ reached getOption(max.print) -- omitted 27821 rows ]]. is it possible to set the maxprint parameter so that R prints all the rows? tia, anjan -- = anjan purkayastha, phd bioinformatics analyst whitehead institute for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
