> x = c(1,2,5,7,9)
> x
[1] 1 2 5 7 9
> x <- 3
> x
[1] 3
> x <- matrix(c(1,5,7,9,12,16,18,0,3), nrow=3,ncol=3)
> x
[,1] [,2] [,3]
[1,] 1 9 18
[2,] 5 12 0
[3,] 7 16 3
> x[,1]
[1] 1 5 7
> x[1,]
[1] 1 9 18
> x[3,3] <- 10
> x
[,1] [,2] [,3]
[1,] 1 9 18
[2,] 5 12 0
[3,] 7 16 10
> x = data.frame(color=c(“Blue”,”Orange”,”Green”), Number=c(1,2,3))
> x
color Number
1 Blue 1
2 Orange 2
3 Green 3
> x$Number
[1] 1 2 3
> time = c(12,5,7)
> new_x = cbind(x,time)
> new_x
color Number time
1 Blue 1 12
2 Orange 2 5
3 Green 3 7
> col1 = c(‘Red’, 4, 7)
> new_x = rbind(x,col1)
> new_x
color Number
1 Blue 1
2 Orange 2
3 Green 3
4 Red 4
> new_x = cbind(new_x,time)
Error in data.frame(…, check.names = FALSE) :
arguments imply differing number of rows: 4, 3
> time = c(1,2,3,4)
> new_x = cbind(new_x,time)
> new_x
color Number time
1 Blue 1 1
2 Orange 2 2
3 Green 3 3
4 Red 4 4
> exprdata = read.table(“
+ RUN3_all_R1-R16_analysis”)
Error in file(file, “rt”) : cannot open the connection
In addition: Warning message:
In file(file, “rt”) : cannot open file ‘
RUN3_all_R1-R16_analysis’: No such file or directory
> exprdata = read.table(“RUN3_all_R1-R16_analysis”)
Error in file(file, “rt”) : cannot open the connection
In addition: Warning message:
In file(file, “rt”) :
cannot open file ‘RUN3_all_R1-R16_analysis’: No such file or directory
>
>
> exprdata = read.table(“RUN3_all_R1-R16_analysis.txt”, header =T)
> head(exprdata)
R1 R5 R9 R13 R2 R6 R10 R14 R3 R7 R11 R15 R4 R8 R12 R16
AAC1 543 521 602 554 1046 775 1211 1159 1019 1111 1273 1390 1102 968 1310 480
AAC3 72 53 141 63 44 29 57 27 23 32 63 29 13 30 50 30
AAD10 584 379 317 324 393 293 513 380 336 359 412 347 312 333 369 171
AAD14 529 481 564 485 350 365 550 384 316 393 348 419 364 384 353 304
AAD15 2 0 4 2 1 1 4 0 0 4 1 2 0 2 1 0
AAD3 468 389 303 407 318 304 320 288 283 323 319 269 249 284 339 255
> plot(exprdata$R1, exprdata$R5, log=’xy’)
Warning messages:
1: In xy.coords(x, y, xlabel, ylabel, log) :
273 x values <= 0 omitted from logarithmic plot
2: In xy.coords(x, y, xlabel, ylabel, log) :
272 y values <= 0 omitted from logarithmic plot
> plot(exprdata$R1, exprdata$R5, log=’xy’, pch=20, col=rgb(0,0.5,0.8,0.5))
Warning messages:
1: In xy.coords(x, y, xlabel, ylabel, log) :
273 x values <= 0 omitted from logarithmic plot
2: In xy.coords(x, y, xlabel, ylabel, log) :
272 y values <= 0 omitted from logarithmic plot
> plot(exprdata$R1, exprdata$R5, log=’xy’, pch=20, col=rgb(0,0.5,0.8,0.5), xlim=c(0.0001,100000),ylim(0.0001,100000))
Error in ylim(1e-04, 1e+05) : could not find function “ylim”
In addition: Warning messages:
1: In xy.coords(x, y, xlabel, ylabel, log) :
273 x values <= 0 omitted from logarithmic plot
2: In xy.coords(x, y, xlabel, ylabel, log) :
272 y values <= 0 omitted from logarithmic plot
> plot(exprdata$R1, exprdata$R5, log=’xy’, pch=20, col=rgb(0,0.5,0.8,0.5), xlim=c(0.0001,100000),ylim(0.0001,100000))
Error in ylim(1e-04, 1e+05) : could not find function “ylim”
In addition: Warning messages:
1: In xy.coords(x, y, xlabel, ylabel, log) :
273 x values <= 0 omitted from logarithmic plot
2: In xy.coords(x, y, xlabel, ylabel, log) :
272 y values <= 0 omitted from logarithmic plot
> plot(exprdata$R1, exprdata$R5, log=’xy’, pch=20, col=rgb(0,0.5,0.8,0.5), xlim=c(0.0001,100000),ylim=c(0.0001,100000))
Warning messages:
1: In xy.coords(x, y, xlabel, ylabel, log) :
273 x values <= 0 omitted from logarithmic plot
2: In xy.coords(x, y, xlabel, ylabel, log) :
272 y values <= 0 omitted from logarithmic plot
> plot(exprdata$R1, exprdata$R5, log=’xy’, pch=20, col=rgb(0,0.5,0.8,0.5), xlim=c(0.0001,100000),ylim=c(0.0001,100000),xlab=’Replicate1′, ylab=’Replicate2′, cex.lab = 1.5)
Warning messages:
1: In xy.coords(x, y, xlabel, ylabel, log) :
273 x values <= 0 omitted from logarithmic plot
2: In xy.coords(x, y, xlabel, ylabel, log) :
272 y values <= 0 omitted from logarithmic plot
> plot(exprdata$R1, exprdata$R5, pch=20, col=rgb(0,0.5,0.8,0.5), xlim=c(0.0001,100000),ylim=c(0.0001,100000),xlab=’Replicate1′, ylab=’Replicate2′, cex.lab = 1.5)
> plot(exprdata$R1, exprdata$R5, pch=20, col=rgb(0,0.5,0.8,0.5), xlim=c(0.0,10000),ylim=c(0.0,10000),xlab=’Replicate1′, ylab=’Replicate2′, cex.lab = 1.5)
> plot(exprdata$R1, exprdata$R5, pch=20, col=rgb(0,0.5,0.8,0.5), xlim=c(0.0,10000),ylim=c(0.0,10000),xlab=’Replicate1′, ylab=’Replicate2′, cex.lab = 1.5, main=’Data Reproducibility’)
> dev.copy2pdf(file = “Plot.pdf”,useDIngbats= F)
Error in device(…) : unused argument (useDIngbats = FALSE)
> dev.copy2pdf(file = “Plot.pdf”,useDingbats= F)
X11cairo
2
> dev.off()
null device
1
>
