similar to: Error message when creating a dataframe

Hi, I have a file of the following type: id a b 1 0.5 5 2 0.7 15 3 1.6 7 4 0.5 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

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

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

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

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

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: c1 c2 ... 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 -- ===================================

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 --

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

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

Hi, I'm planning to access R from my perl scripts. The only noteworthy bridge seems to be Statistics-R-0.03<http://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 --

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

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,

Hi, my data table has 38939 rows. R prints the first 11111 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

I have a data matrix: repeat1 repeat2 1 30 34 2 12 23 3 50 13 4 56 98 . . . 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

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

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

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

Hi, I have a data-frame r (shown below is a subset) with the following column names: date time sample vct norm hct deltact $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

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 -- =============================

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: 10000, 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, .......10000? Thanks for your help. Anjan ID