I am trying to design a matrix, but I got the following error. Please help me to understand this error.

# > design <- matrix(data=0,nrow=ncol(gene expression data), ncol=2)
> rownames(design) <- colnames(gene expression data)
> colnames(design) <- c("Carcinoma","Normal")
> cSamples <- rownames(phenodata)[grep("Tumor",HB$Condition)]
> nSamples <- rownames(phenodata)[grep("Non_neoplastic",HB$Condition)]
> design[cSamples,"Carcinoma"] <- 1
**Error in `[<-`(`*tmp*`, cSamples, "Carcinoma", value = 1) : 
  subscript out of bounds**

# This is my phenodata

Sample_id   Condition   Patient Batch
P105A   Non_neoplastic  P105    A
P105D    Tumor                  P105    A
P106A   Non_neoplastic  P106    B
P106D   Tumor                  P106     B 
P112A   Non_neoplastic  P112    C
P112D   Tumor                  P112         C 
P131A   Non_neoplastic  P131    D
P131D   Tumor                   P131    D
P138A   Non_neoplastic  P138    E
P138D   Tumor                  P138     E
P140A   Non_neoplastic  P140    F
P140D   Tumor                  P140     F
P152A   Non_neoplastic  P152    G
P152D   Tumor                  P152     G
P157A   Non_neoplastic  P157    H
P157D   Tumor                  P157     H
P158A   Non_neoplastic  P158    I
P158D   Tumor                  P158         I
P161A   Non_neoplastic  P161    J
P161D   Tumor                   P161    J
P16A    Non_neoplastic  P16         K
P16D    Tumor                    P16             K
P170A   Non_neoplastic  P170     L
P170D   Tumor                   P170    L
P171A   Non_neoplastic  P171    M
P171D   Tumor                   P171    M
P176A   Non_neoplastic  P176    N
P176D   Tumor                    P176   N
P179A   Non_neoplastic  P179    O
P179D   Tumor                   P179    O
P49A    Non_neoplastic  P49     P
P49D    Tumor                   P49         P
P62A    Non_neoplastic  P62         Q
P62D    Tumor                   P62         Q
P6A        Non_neoplastic    P6        R
P6D         Tumor                   P6           R
P75A    Non neoplastic  P75     S
P75D    Tumor                   P75         S
P94A    Non_neoplastic  P94         T
P94D    Tumor                   P94         T
P99A    Non_neoplastic  P99         U
P99D    Tumor                   P99     U

There are examples of how to construct design matrices in the limma and edgeR documentation and it is much easier than what you are currently attempting. Your Tumor and Non_neoplastic samples are apparently paired by patient, so the design matrix would be:

design <- model.matrix(~ Condition + Patient, data=HB)