Quantile Normalization in R and output data
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4.0 years ago
bk11 ▴ 60

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.

R Data normalization • 2.6k views
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1
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colnames( data_norm ) <- colnames( data_mat )
rownames( data_norm ) <- rownames( data_mat )

Is this microarray data? If so, I suggest you use limma.

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Thank you! No, these are FPKM values of genes expressed in different cell types. I am trying to do normalization among inter transcripts.

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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.

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