row t test with biocLite(genefilter)
1
0
Entering edit mode
5.8 years ago

I'm trying to run a t test on 2 groups of samples for a list of variables. My dataset (=df) looks like this: 

GeneName  group1  group1  group1  group2  group2  group2

gene1

gene2

gene3

...

I want to obtain p value for t test comparing for each row (gene) the values of group1 vs group2.

I tried to use the rowttests() function of genefilter package for bioconductor as such: 

df$ttest <- rowttests(df, factor(c(group1, group2)))

I'm getting the following error: 

Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘rowttests’ for signature ‘"data.frame", "factor"’

 

What am I doing wrong?

Thanks

row t test genefilter r • 4.3k views
ADD COMMENT
0
Entering edit mode
df$ttest <- rowttests(as.matrix(df[,-1]), factor(c(0,0,0,1,1,1))

gives the following error:

Error in rowcoltt(x, fac, tstatOnly, 1L) :
  Invalid argument 'x': must be a real matrix.
ADD REPLY
0
Entering edit mode

So throw an as.double() in there.

ADD REPLY
0
Entering edit mode

Could you be more specific? (I'm beginner in R)

ADD REPLY
0
Entering edit mode

This is going to get messy, but the general idea is:

df$ttest <- rowttests(matrix(as.double(unlist(df[,-1])), ncol=6), factor(c(0,0,0,1,1,1))

Or something along those lines. BTW, don't worry about the unlist() part, it just converts your data.frame into a vector (data.frames are actually a special kind of list in R).

ADD REPLY
1
Entering edit mode
5.8 years ago
> showMethods(rowttests)
Function: rowttests (package genefilter)
x="ExpressionSet", fac="character"
x="ExpressionSet", fac="factor"
x="ExpressionSet", fac="missing"
x="matrix", fac="factor"
x="matrix", fac="missing"


So, I suspect that something like this will work:

df$ttest <- rowttests(as.matrix(df[,-1]), factor(c(0,0,0,1,1,1))
ADD COMMENT

Login before adding your answer.

Traffic: 1286 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6