I have used this command
plot(log.norm.counts.a[,1:2], cex=.1)
but it gives following error
Error in xy.coords(x, y, xlabel, ylabel, log) : 'x' and 'y' lengths differ
I can't make changes in the file.
anyone know how to solve, like skip ids which are missing.
•
written
by
yusuf •
2 answers
Try this code. It should solve your problem
data <- read.csv("~/Desktop/my_data.csv", header=TRUE)
dim(data)
rnames <- data[,1] # assign labels in column 1 to "rnames"
mat_data <- data.matrix(data[,2:ncol(data)]) # transform column 2-5 into a matrix
rownames(mat_data) <- rnames
mat_data # this is only matrix now with dimension n rows and 12 column
x1 <- mat_data[,1:6] # assigning first 6 cols to x1
y1 <- mat_data[,7:12] # assigning seventh to 12 cols to x1
install.packages("matrixStats")
library(matrixStats)
x2 <- rowSds(x1) # standard deviation from x1
y2 <- rowSds(y1) # standard deviation from y1
plot(x2,y2) # for plot
•
written
by
kashiff007
Hi thankyou for your reply
I want to plot SD of two groups of files, with different length
I have slightly solved this by
Y2 <- as.data.table((log.norm.counts.a[,1:6]), keep.rownames = "geneid")
X2 <- as.data.table((log.norm.counts.b[,1:6]), keep.rownames = "geneid")
m3 <- merge(X2,Y2,by=c("geneid"))
head(m3)
dim(m3)
[1] 1500 13
X1 <- m3[,2:7]
head(X1[,1:6])
Y1 <- m3[,8:13]
head(Y1)
but when i try
a<- as.data.table(rowSds(X1))
b<- as.data.table(rowSds(Y1))
plot(a,b)
or
plot(rowSds(m3[,2:7]),rowSds(m3[,8:13]))
it gives error
Error in rowVars(x, rows = rows, cols = cols, na.rm = na.rm, center = center, :
Argument 'x' must be a matrix or a vector.
even
class(m3)
[1] "matrix"
Have you checked the first few lines of "m3" matrix. what is your head(m3) output?
yes
> head(m3)
geneid FP13w0L.x FP20w0L.x FP27w0L.x FP39w0R.x FP46w0R.x FP7w0L.x FP13w0L.y
1: ENSG00000000003 5.832952 5.702980 5.890075 5.429769 6.197564 5.405774 6.093247
2: ENSG00000000005 0.000000 4.092157 2.959349 2.626327 1.978803 2.133864 0.000000
3: ENSG00000000419 8.154151 7.716715 8.377897 8.100886 8.392561 8.289250 8.287379
FP20w0L.y FP27w0L.y FP39w0R.y FP46w0R.y FP7w0L.y
1: 5.894538 6.105176 5.741960 6.249536 5.527603
2: 4.297580 3.116547 2.726263 2.077238 2.933729
3: 7.738360 8.420916 8.152382 8.435377 8.327208
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You can make changes in the object you create by reading the file. Please search Stack Overflow to understand how to manipulate data frames.
Can you show us a subset of your dataframe ?
The error message say that you do not have the same length between
log.norm.counts.a[,1]andlog.norm.counts.a[,2]. Have you tried to check the content of these two columns ?