search for: salsburg

How do I manipulate the read.table function to read in only the 2nd column??? [[alternative HTML version deleted]]

I have a data frame with the following dimensions 217 x 5 I want to create two data frames from the original. 1) One containing every tenth row of the original data frame 2) Other containing the rest of the rows. How do I do this? I've tried subset() and calling the index. thank you in advance, [[alternative HTML version deleted]]

I have a very large matrix. I would like to display the variance across each row. In other words, I want to output a vector containing the values of variance across row. When I use the function var(), it seems to give me the variability of each column. Any ideas?? [[alternative HTML version deleted]]

I am getting an error message, which I do not know the source to. I have a matrix SAMPLES that has preexisting rownames that I would like to change. GENE_NAMES contains these rownames. > rownames(SAMPLES) = GENE_NAMES Error in "dimnames<-.data.frame"(`*tmp*`, value = list(list(V1 = c(3843, : invalid 'dimnames' given for data frame > dim(SAMPLES) [1] 12626

I am trying to find out if R can recognize specific criteria for removing rows (i.e. a prexisting function) I have a matrix myMatrix that is 12000 by 20 I would like to remove rows from myMatrix that have: -999 across all columns -999 across all columns but one -999 across all columns but two -999 across all columns but three -999 across all columns but four -999 across all columns but five

...ay/matrix? (Michael) 30. Re: returning the largest element in an array/matrix? (Gabor Grothendieck) 31. Making an S3 object act like a data.frame (hadley wickham) 32. Re: Making an S3 object act like a data.frame (Gabor Grothendieck) 33. reading in only one column from text file (mark salsburg) 34. reading in only one column from text file (mark salsburg) 35. how to use the rpart function? (Michael) 36. Re: Making an S3 object act like a data.frame (hadley wickham) 37. Re: reading in only one column from text file (Seth Falcon) 38. Fwd: reading in only one column from text fil...

I have a vector of size 217 called "A". the values of A are not sorted and range from 0 to 1 (normalized) I am having difficulty writing a program to create a new vector "B" where if A's value is 0< A <=0.333 then B is 0 if A's value is 0.333< A <=0.666 then B is 1 if A's value is 0.666< A <=1 then B is 2 so if A is 0.22 0.999 0.444 0 B would

I'm having this error when I try to output out a gene expression data frame Error in file(file, ifelse(append, "a", "w")) : unable to open connection In addition: Warning message: cannot open file 'SAMPLES.txt' when issuing the command: write.table(SAMPLES, file = "SAMPLES.txt") write.table(SAMPLES) will work fine, but when I specify a

Dear group, I would like to generate a 1000 random rows from a MATRIX with dimensions 12,000 by 20 (i.e. to generate a 1000 by 20 matrix of random rows) Does the function sample() work for this??? thank you in advance [[alternative HTML version deleted]]

I have two objects, one matrix and one vector. I want to use my vector to subset certain values out of my matrix. For example: I want to tell R, to select out all rows in myMatrix into a new myMatrix2 IF that corresponding row is less than a 0.5 in myVector. So: myMatrix = a matrix of 8000 by 20 myVector = vector of 8000 myMatrix2 = a matrix of < 8000 by 20 (based on selection criteria in

ok I created a matrix C with A B C A1 B1 C1 .................................. ................................. the columns contain the gene expression values.. I ran the following t.test: apply(C, 1, function(x) t.test( x[1:3], x[4,6] )$p.value ) which outputs out 16063 pvalues (the number of rows) I just want to output 3 pvalues showing if A's column is different from A1

I have a vector of values (about 8000 obs between 0 and 1). I want to display a histogram as follows: value of vector ( bw 0 and 1) | | | | | |______________________________________ all 8000 obs. So that each section of the x axis corresponds

I sent this to Bioconductor, but I think it is more of an R listserv question, because of memory allocation trouble I am having trouble getting the function heatmap() to work on the following gene expression > dim(SAMPLES_log) [1] 12626 20 sample1 sample2...................sample20 gen1 gen2 gen3 .... gen12626 I have converted SAMPLES_log to a numeric matrix using:

Can someone please refer me to a function or method that resolves this structuring issue: I have two matrices with identical colnames (89), but varying number of observations: matrix A matrix B 217 x 89 16063 x 89 I want to creat one matrix C that has both matrices adjacent to one another, where matrix A is duplicated many times to

I cannot find in the literature a way to conduct the following t.test on 2 objects, A and B A B col1 col2 col3 col1 col2 col3 Where col(i)'s name is identical in both A and B (they are names of tissues). How do I test (t.test) if each tissue across the object is signifanctly different?? (i'm pretty sure I have to use tapply())