Quantile Normalization in R and output data
Hi all, I am having a problem for not getting rows and columns names in my output.
data=read.csv("bk.txt", sep="\t", header=T)
head(data)
X adult.endothelial.progenitor.cell alternatively.activated.macrophage
1 ABCG4 1.17 1.00
2 AP003391.1 1.00 1.00
3 ATP5L 170.36 200.45
4 BCL9L 17.52 1.74
5 BMPR1APS2 1.04 1.05
6 C2CD2L 4.44 11.20
rownames(data) <- data[,1]
data_mat <- data.matrix(data[,-1])
head(data_mat)
adult.endothelial.progenitor.cell alternatively.activated.macrophage
ABCG4 1.17 1.00
AP003391.1 1.00 1.00
ATP5L 170.36 200.45
BCL9L 17.52 1.74
BMPR1APS2 1.04 1.05
C2CD2L 4.44 11.20
data_norm <- normalize.quantiles(data_mat, copy = TRUE)
head(data_norm)
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
[1,] 1.316610 1.002034 1.002034 1.006864 1.201017 1.000169 1.316610 1.001017
[2,] 1.003051 1.002034 1.002034 1.006864 1.002034 5.781186 1.002034 1.001017
[3,] 219.738136 219.738136 87.607966 219.738136 219.738136 87.607966 219.738136 219.738136
[4,] 12.947627 1.983136 5.781186 1.201017 4.649492 19.805254 2.767627 5.781186
[5,] 1.201017 1.133051 1.316610 1.006864 1.002034 1.092881 1.002034 1.001017
[6,] 2.767627 25.918475 16.030169 4.649492 25.918475 2.150000 16.030169 2.767627
Can some one help me in getting the rows and columns info in my output normalized data? I will appreciate your help. Thanks.
0 answers
No answers yet.
Log in to answer this question.
Is this microarray data? If so, I suggest you use limma.
Thank you! No, these are FPKM values of genes expressed in different cell types. I am trying to do normalization among inter transcripts.
What you want to do? Differential expression? FPKM is not recommend as within-sample normalization (TPM is better) and, depending on the software you intend to use for differential expression analysis, you should input raw counts, not normalized values.