matrix transpose in R

Hi friends,

Using some commands I normalized an array with mas5, may you please tell me exactly with which commands I can transpose the produced matrix. text file in R?

For example I changed the directory to where I saved my produced file, opened R and typed:

> t()
Error in t.default() : argument "x" is missing, with no default

microarray affy r mas5

• 6,937 views • link

updated 3.7 years ago by Ram

• written 11.1 years ago by zizigolu

Hello sarah!

We believe that this post does not fit the main topic of this site.

This is solely programming question and belongs to stack overflow. Or you can simply solve it yourself by typing ?t and reading the documentation.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

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written 11.1 years ago by PoGibas

ok as you order!!

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written 11.1 years ago by zizigolu

............

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written 11.1 years ago by zizigolu

2 answers

Sarah,

To transpose a matrix, the function is t()

Suppose your matrix is saved in an object matrix

# transposing a matrix
transpose_matrix <- t(matrix)

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updated 3.7 years ago by Ram

• written 11.1 years ago by Deepak Tanwar

Hi Deepak,

I had a file. First I normalized GSE33964, with below commands

library(affy)
library(methods)

inFilePattern = "*CEL.gz"
outFilePath = "GSE33964.matrix"
fileNames = list.files(pattern=glob2rx(inFilePattern))
rawData = ReadAffy(filenames=fileNames)
eset <- mas5(rawData)
write.exprs(eset, file=outFilePath, col.names=NA)

Now I have a file containing NA...

I typed these codes to transpose that but no new file was produced or no changed I saw in primary file. then where is transposed matrix please or if I did right?

changedir

GSE33964_new <- t(GSE33964)
GSE33964 <- matrix(1:30, 5, 6)
tGSE33964 <- t(GSE33964) ##-- i.e., GSE33964[i, j] == tGSE33964[j, i] for all i,j :
for(j in seq(ncol(a)))
  if(! all(GSE33964[, j] == tGSE33964[j, ])) stop("wrong transpose")
  transpose_GSE33964 <- t(GSE33964)

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updated 3.7 years ago by Ram

• written 11.1 years ago by zizigolu

t() is correct, but you (A) have to have the matrix loaded and (B) tell t() what it is. For example, if your matrix is named m, then, m_new <- t(m).

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updated 3.7 years ago by Ram

• written 11.1 years ago by Devon Ryan