Displaying 20 results from an estimated 300 matches similar to: "Newbie: Incorrect number of dimensions"
2008 Mar 02
2
Variance Calculation in R
Hello,
Thanks everyone for helping me with the previous queries.
step 1: Here is the orginal data: short sample
ProbeID Sample_1_D Sample_1_C Sample_2_D Sample_2_C
1 224588_at 2.425509867 11.34031409 11.46868531 11.75741478
step 2: i calculate the variance of the sample using this R code
x<-1:20000
y<-2:141
data.matrix<-data.matrix(data[,y])#create data.matrix
2008 Mar 04
2
paired or one-sample t-Test
Hi Guys,
I am having a real hard time trying to figure out for microarry.
Here is my code
One-Sample t-Test
dim(data.sub)
[1] 10000 140 ##there are 10000 probesets and 140 columns
hist(data.sub) ## Histogram. Identify if the probesets are normal
distributed
q<-rnorm(10000) ##generate 10000 random, normal distributed values
qqplot(data.sub,q)) ##Show the plot of the probeset
2010 Mar 03
1
Help with multtest (rawp2adjp)
Hello R experts,
I am trying to analyze this dataset and am stuck on this problem for quite
some time now.
I am using mt.rawp2adjp.
the output that came out was a matrix with two colums since I had asked it
to calculate the adjusted p values using one method.
so it has the two columns as: rawp BH
I combined these using cbind with my actual dataframe.
checked using head all was fine.
thereafter I
2010 Jul 13
6
permutation-based FDR
Hola a todos,
Tengo un pequeño problemilla...
Tengo unas 9000 variables que he contrastado con 1 en concreto con el test
de wilcoxon. He calculado el p-valor, y queria corregirlo con el
permutation-based FDR. He encontrado una funcion con R comp.fdr()que hace
esta corrección, pero te pide que le pongas las variables con las
observaciones y te hace el test (según he entendido). Yo solo quiero
2008 Feb 24
3
Newbie: Where is lmFit function?
Hi Everyone,
I am trying to use lmFit function; however, i cannot find it function
anywhere.
I have been trying to find the function in Bioconductor and elsewhere. I
re-install bioconductor source, update package and update R as well. no luck
Is there a command in R where i can just type, and it will download it for
me?
--
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2008 Mar 02
4
Newbie:Export Data into Excel from R
Hi,
All i want is to export my list into c: drive and save it as csv file and
manually import into Excel.
I have the read the article but i am having issues
http://pbil.univ-lyon1.fr/library/base/html/write.table.html
> excel<-write.table(probe_gene, file = "c:\foo.csv", sep = ",", col.names =
> NA)
Error in file(file, ifelse(append, "a", "w"))
2008 Mar 03
3
R data Export to Excel
Here is my R Code
x<-1:20000
y<-2:141
data.matrix<-data.matrix(data[,y])#create data.matrix
variableprobe<-apply(data.matrix[x,],1,var)
variableprobe #output variance across probesets
hist(variableprobe) #displaying histogram of variableprobe
write.table(cbind(data[1],
Variance=apply(data[,y],1,var)),file='c://variance.csv')
#export as a .csv file.
Output in Excel
all in 1
2008 Mar 08
3
expression matrix
Hello,
I am to run this R script but i keep getting this error.
> expr<-exprs(golubMerge)
Warning message:
The exprSet class is deprecated, use ExpressionSet instead
I tried to find information on the website but no luck. (exprSet...etc)
thank you.
--
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2008 Mar 03
3
Calculating the t-test for each row
Hi Everyone,
I need some simple help.
Here are my codes
##########will give me 10000 probesets####################
data.sub = data.matrix[order(variableprobe,decreasing=TRUE),][1:10000,]
dim(data.sub)
data_output<-write.table(data.sub, file = "c://data_output.csv", sep = ",",
col.names = NA)
When i export to excel, it shows me this. This is just a short version.
There
2008 Feb 23
3
exprs function download
Hi,
I am supposed to use exprs as a function. Where can i download exprs
function? I tried searching at bioconductor and seach engine but no luck. Is
it located in one of the library in R?
thanks.
C
--
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Sent from the R help mailing list archive at Nabble.com.
2008 Mar 09
2
p-adjust using Benjamn and Hochberg
Hello,
I am trying to use the p.adjust function for multiple testing.
here is what i have
9997 201674_s_at 0.327547396
9998 221013_s_at 0.834211067
9999 221685_s_at 0.185099475
I import them from excel have have the gene symbol as well as the pvalue
here is the issue
> pa<-p.adjust(pt,method="BH")
Error in p[nna] : object is not
2011 Mar 08
1
Multiple testing corrections on very large vector
Hello all,
I am calculating probabilities of association for terms in the
GeneOntology database. I have ~4e7 probabilities and I would like to correct
for multiple testing. At the moment I have something like the following:
pv is a vector containing my 4e7 probabilities.
To run the multiple testing corrections I do:
mt <- mt.rawp2adjp(pv, proc="BH")
Because of the size of
2008 Mar 05
4
Excel export into R
Hello,
I have this in excel
Control
543_BU
123_AT
432_CU
I want to be able to import to R so that it will read like this
c<-c("543_BU","123_AT","432_CU")
output:
[1] "543_BU" "123_AT" "432_CU"
This is just a short version. I have about 200000 rows and i need a simpler
way instead of typing each one.
thanks
--
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2011 Apr 21
2
HDT 0.5.0 is out
Just a quick note to tell that I did release HDT 0.5.0.
Main feature of this release is the dumping of the detected components
over TFTP (meaning PXE is _mandatory_ to work).
I did fix also the auto mode where more combinations didn't worked as
expected.
I invite people reading this page that speaks about the dump feature :
http://www.hdt-project.org/wiki/Dump
But also, this one which
2011 Apr 21
2
HDT 0.5.0 is out
Just a quick note to tell that I did release HDT 0.5.0.
Main feature of this release is the dumping of the detected components
over TFTP (meaning PXE is _mandatory_ to work).
I did fix also the auto mode where more combinations didn't worked as
expected.
I invite people reading this page that speaks about the dump feature :
http://www.hdt-project.org/wiki/Dump
But also, this one which
2004 Jan 20
1
Re: Need help on how to list functions from a loaded package...
To All
How does one get a list of functions from a loaded package so that one can
then get the appropriate help for each of the functions. Currently my
method is
based on a lot of trial-and-error.
Here's an example of what I mean...
>From this forum I learn that an interesting package called "multtest" exists
on Bioconductor.
I then use R Console's "Packages" --
2008 Feb 19
1
Calculating the distance samples using distance metics method
***********reading in data**********
data<-read.table("microarray.txt",header=T, sep="\t")
head(data)
dim(data)
attach(data)
***********creating matrix and calculating variance across probesets********
x<-1:20000
y<-2:141
data.matrix<-data.matrix(data[,y])
variableprobe<-apply(data.matrix[x,],1,var)
hist(variableprobe)
**************filter out low
2009 Sep 12
0
[PATCH 11/13] nv50: add support for light-twoside
---
src/gallium/drivers/nv50/nv50_program.c | 19 +++++++++++++++++++
src/gallium/drivers/nv50/nv50_state.c | 4 +++-
2 files changed, 22 insertions(+), 1 deletions(-)
diff --git a/src/gallium/drivers/nv50/nv50_program.c b/src/gallium/drivers/nv50/nv50_program.c
index feb1504..39c3afc 100644
--- a/src/gallium/drivers/nv50/nv50_program.c
+++ b/src/gallium/drivers/nv50/nv50_program.c
@@
2008 Jul 30
1
model mix problem. FALSE CONVERGENCE
Hi R users
I try to use the lme but I can?t!!!!!
My script is (some words in french, sorry!!):
rm(list=ls(all=TRUE)) #Efface tous les objets en m?moire pour ?viter des
erreurs
library(MASS) #Chargement des Librairies
library(car)
library(Hmisc)
library(tkWidgets)
library(svDialogs)
library(multtest)
library(nlme)
#Rep <- "C:/Documents and Settings/U3M/Bureau/steph/Scripts
2007 Jun 14
1
Wilcoxon test on data matrix
Dear everyone,
I am trying to do a Wilcoxon one-sided test on my gene expression data.
These are the data i have in R:
data.matrix (matrix, numeric) containing all gene expression data (42 rows=genes, 42 columns=tumors), no column header or row names
data.cl (vector, numeric) consisting of 42 0's and 1's to indicate class 0 or class 1 for each column in data.matrix
I want to do a