Thanks so much, will check it out!
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Gregor Rot
DESeq2 count matrix read in
Dear all,
From the DESeq2 guide (http://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#countmat) I try to read a count matrix in from a TAB separated file:
cts <- as.matrix(read.csv("data.tab", sep="\t", row.names="gene_name"))
However I see that as.matrix causes the values to be "strings" in R?
head(cts, 3)
entrez_id CON6_A CON6_B CON6_C AMD6_A AMD6_B
0610005C13Rik "71661" " 0" " 0" " 13" " 0" " 0"
0610007P14Rik "58520" " 1224" " 2002" " 1931" " 1830" " 1155"
0610009B22Rik "66050" " 67" " 59" " 41" " 27" " 54
If I don't convert to matrix with:
cts <- read.csv("data.tab", sep="\t", row.names="gene_name")
All looks good:
entrez_id CON6_A CON6_B CON6_C AMD6_A AMD6_B AMD6_C
0610005C13Rik 71661 0 0 13 0 0 16
0610007P14Rik 58520 1224 2002 1931 1830 1155 1596
0610009B22Rik 66050 67 59 41 27 54 23
Is casting to as.matrix a must for DESeq2? Could someone advise?
Thanks,
Gregor
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Ram
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Gregor Rot
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Gregor Rot
4 answers
DESeq2 can also take a data.frame but it must be all-numeric so you would need to move the gene column to rownames:
rownames(cts) <- cts[,1]
cts[,1] <- NULL
dds <- DESeqDataSetFrommatrix(countData=cts, ...)
You see your matrix becoming type character after as.matrix (check with typeof(cts)) because the gene column is of type character and a matrix in R can only hold one type of data whereas a data.frame could hold multiple types. Since character is more flexible that numeric (aka double) the matrix gets coerced to character. See for more info on all that: http://adv-r.had.co.nz/Data-structures.html
You also want read.csv(..., header=TRUE) to move the csv header to data.frame/matrix colnames.
Your count matrix might have quotation marks in it, values might be getting imported as strings and converted to factors:
> x <- data.frame(A=factor(c(0,0,0,0,1,3,3,4)), B=factor(c(0,1,0,1,2,3,4,5)))
> x <- data.frame(A=factor(c(0,0,0,0,1,3,3,4)), B=factor(c(0,1,0,1,2,3,4,5)))
> print(x)
A B
1 0 0
2 0 1
3 0 0
4 0 1
5 1 2
6 3 3
7 3 4
8 4 5
> as.matrix(x)
A B
[1,] "0" "0"
[2,] "0" "1"
[3,] "0" "0"
[4,] "0" "1"
[5,] "1" "2"
[6,] "3" "3"
[7,] "3" "4"
[8,] "4" "5"
Check your data file for quotation marks around the numbers. It could be something to do with how the file is being imported. Try "read.table" and specify the quoting character (quote="\"") .
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adam.faranda
Thank you for your answer. My file is without any quotes and is very simple:
gene_name entrez_id CON6_A CON6_B CON6_C AMD6_A AMD6_B AMD6_C
0610005C13Rik 71661 0 0 13 0 0 16
0610007P14Rik 58520 1224 2002 1931 1830 1155 1596
0610009B22Rik 66050 67 59 41 27 54 23
0610009L18Rik 66838 55 34 44 18 13 49
0610009O20Rik 66839 241 212 257 432 188 239
What would be the right way to read this data in? Thanks
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Gregor Rot
That's interesting, maybe there is some other reason that these values are being converted to factors?
can you check the results of class(cts$CON6_A) and post?
Load the data in as you have been, without casting to a matrix.
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adam.faranda
read.csv can read tab-delimited files fine, when the sep parameter is tab (the OP said that the file is tab-delimited).
ttt <- matrix(runif(100),nrow=10)
write.table(ttt, "ttt.tsv", sep="\t")
check_res <- read.csv("ttt.tsv", sep="\t")
check_res[1:4,1:4]
V1 V2 V3 V4
1 1 11 21 31
2 2 12 22 32
3 3 13 23 33
4 4 14 24 34
Hi Gregor!
It is not necesary that your count matrix has a class of matrix to use DESeq2. In my earlier analysis I was using DESeq2 and after importing my data into R (using tximport package) a list was created. My raw counts matrix was stored in such list with a class of matrix. I re-coded the count matrix as a data frame since I feel more comfortable working with df instead of matrices. After running DESeqDataSetFromMatrix function everything ran without warnings.
Rodo
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