Error occured in designing a matrix
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2.7 years ago
rishav513 ▴ 30
> 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",phenodata$Condition)]
> nSamples <- rownames(phenodata)[grep("Non_neoplastic",phenodata$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

R • 625 views
Entering edit mode

Cross-posted to Bioconductor

Entering edit mode

Have you tried trouble shooting? Check the dimensions of all the things you're creating. i.e. length(cSamples), etc. Also, is this: "ncol(gene expression data)" a shorthand? If not, that line should fail because you can't give multiple arguments separated by a space in that function.

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There is no space between gene expression data, it is like this "geneexpressiondata"


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