Can I ask, when I run the below code:
library(qvalue)
pvals
<-c(0.01,0.02,0.03,0.10,0.67,0.08,0.55,0.10,0.81,0.08,0.94,0.10,0.81,0.08,0.72,0.10,0.22,0.08,0.72,0.01,0.02,0.03,0.04,0.05,0.06,0.07,0.01,0.02,0.03,0.10,0.67,0.08,0.55,0.10,0.81,0.08,0.94,0.10,0.81,0.089,0.72,0.10,0.22,0.08,0.72,0.01,0
Dear all,
I am hoping to use the mt.maxT package, so I'm trying to understand how the
maxT algorithm works in the multtest package.
I have an example of data:
SNP1 p value= 0.02
SNP1 permutation p values = 0.03, 0.03, 0.03, 0.04, 0.04.
SNP2 p value =0.03
SNP2 permutation p values = 0.4,0.5,0
Hi all,
I want to associate mortality with ~100K SNPs, in 6,500 samples that are
divided up into 60 breeds.
So it's important to account for population stratification in my analysis.
I'm using egscore (the eigenstrat method) for the association (and I've
tried using the polygen and grammar packa
Having a problem with convert.snp.ped in GenABEL (on linux).
My map file looks like this (tab-separated) (called Genotype.map)
chrom name position
13 SNP1 39703523
My ped file looks like this (Called Genotype.ped)
PF1 PF1 0 0 2 -9 C C
PF2 PF2 0 0 2 -9 C A
PF3 PF3 0 0 1 -9 C C
PF4 PF4
on (or many questions ... ).
>
> So your data should look like:
>
> V1 V2 V3 Survival Event
> ann 13 WTHomo 41
> ben 20 NA 51
> tom 40 Variant 6
Hi all,
I have a data set like this:
Test.cox file:
V1V2 V3 Survival Event
ann 13 WTHomo 41
ben 20 *51
tom 40 Variant 61
where "*" in
Hi all,
I have a data set like this:
Test.cox file:
V1V2 V3Survival Event
ann 13 WTHomo 41
ben 20 *51
tom 40 Variant 61
w
ctly? You probably
> need
>
> list.files(pattern = ".out")
>
> to get started. Then just wrap your script in a function and pass it
> to (s|l)apply something like:
>
> sapply(list.files(pattern = *.out"), function(x) wilcox.test ( ... ) )
>
> Michael
>
Hey guys,
Does anyone have an example of a REALLY simple shell script in R.
Basically i want to run this command:
library(MASS)
wilcox.test(list1,list2,paired=TRUE,alternative=c("greater"),correct=TRUE,exact=FALSE)
in a shell script something like this:
#!/bin/bash
R
library(MASS)
for i in *.ou
Hello
I have two lists of numbers, each list is ~800 numbers long. I want to know
if the two lists are significantly different from each other.
Could anyone suggest what library in R to use?
I think maybe the mann-whitney test, as it is not parametric, but i am
unsure if it is suitable as my list
Hey guys, can anyone help?
i have a sample table:
>table <- structure(c(4, 7, 0.2, 3, .1, 7, 222, 3, 10, 5, 11,
8, 8, 10, 7), .Dim = c(5L, 3L), .Dimnames = list(c("gene1",
"gene2", "gene3", "gene4", "gene5"), c("codon1", "codon2",
"codon3")))
>table
codon1 codon2 codon3
gene14.0
Hey guys,
if i do a correspondance analysis, e.g.:
table <- structure(c(4, 7, 0.2, 3, .1, 7, 222, 3, 10, 5, 11,
8, 8, 10, 7), .Dim = c(5L, 3L), .Dimnames = list(c("gene1",
"gene2", "gene3", "gene4", "gene5"), c("codon1", "codon2",
"codon3")))
Library(ca)
plot(ca(table))
is there a way
Hey i have a similar size dataset and ran into the same problem, but i
found this command works fine:
options(max.print=100)
to fix it?
On Sat, Mar 10, 2012 at 4:35 PM, sybil kennelly wrote:
> Dear all.
>
> I wanted to read in a 20,000 row X 60 column matrix (called "table") into
> R.
>
>
ure to answer your question is like
> buying a new suit then having plastic surgery to make you fit the suit
> rather than having the tailor modify the suit to fit you.
>
> If you can give us more information about what your question is we
> have a better chance of actually helping y
Thank you. Can the chi-squared test compare two matrices that are not the
same size, eg if matrix 1 is a 2 X 4 table, and matrix 2 is a 3 X 5 matrix?
On Fri, Mar 9, 2012 at 4:37 PM, Greg Snow <538...@gmail.com> wrote:
> The chi-squared test is one option (and seems reasonable to me if it
> the t
Many thanks for reply.
I have trouble understanding how to use response, i am sorry.
My question is i have two matrices. I then plot two matrices. Then I have 2
seperate plots. I can color the nodes in the plots in two different colors.
Then, how do i merge the two plots to view one overlapping the
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