Displaying 20 results from an estimated 26 matches for "elenichri".
2010 Mar 09
4
Transfer R workspace on another PC
Hi list!
I have recently tried to take my office work home, meaning that I tried to
transfer my "... .RData" workspace from my PC on my laptop. The office PC
runs on Windows XP and my laptop runs on Windows Vista. I have saved the
workspace at the office PC and kept it in a usb drive. When I tried to open
it on my laptop I got an error: "Fatal Error: Unable to restore saved data
in
2008 Mar 05
2
t.test & p-Value
Hello list,
I am trying to apply the paired t.test between diseased and not diseased
patients to identify genes that are more expressed in the one situation
under the other. In order to retrieve the genes that are more expressed in
the positive disease state I do:
p.values<-c()
for(i in 1:length(Significant[,1])){
p.values[i]<-try(t.test(positive[i,],negative[i,],alternative
2008 Feb 14
4
Kaplan Meier function
Hi all,
I am trying to draw a Kaplan-Meier curve and I found online that Kaplan -
Meier estimates are computed with a function called km in the event package.
Is there an update for that because when I choose to download packages in
R,. there is no package called event, even though I have selected all the
repositories.
Thanks in advance,
Eleni
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2007 Nov 29
1
coloring leaves in clustering
Hello everyone,
I wanted to know if it was possible to change the color of certain leaves in
a hclust object in order to make my graph more readable. I know I can color
certain groups but I would like to enter a vector telling the plot function
which leaves to color in which color.
Thanks in advance,
Eleni
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2008 Jun 10
1
samr result
Hello list!
I have a proble trying to perform a SAM analysis using the function samr
from the samr package. I have put the option *center.arrays=TRUE *in order
to scale all the experiments to median=0. I would like to retrieved the
scaled data but it seems that samr does not return it...Does anyone have any
idea on this?
Thanks a lot!!!
E.
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2008 Jan 31
2
Delete/insert rows in data matrix
Hello all,
I have the following problem. I want to insert blank rows in an data frame
so as to make it comparable with another data frame with more rows. How can
I insert these rows?
If this is not solvable, then, alternatively, is it easy to delete rows from
a data frame?
Thanks for helping,
Eleni
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2008 May 19
1
oligo ids
Dear list,
I am having a set of human oligo ids (H200006022 H200002025 H300004703
H200000442 H200005719 H300018350) which I want to map to Ensembl or RefSeq.
I am sure R has a function to do that. I downloaded the {oligo} package and
tried to use the probeNames function. Although the factor of ologo ids is an
object (as the argument to probeNames should be) I retrieve the following
error:
2008 May 19
0
[BioC] oligo ids
...ady got almost what I wanted. I have some
NA values but I will look if I can find them through bibliography or an
external tool.
Best Regards,
Eleni
On Mon, May 19, 2008 at 6:07 PM, Sean Davis <sdavis2@mail.nih.gov> wrote:
> On Mon, May 19, 2008 at 10:47 AM, Eleni Christodoulou
> <elenichri@gmail.com> wrote:
> > Dear list,
> >
> > I am having a set of human oligo ids (H200006022 H200002025 H300004703
> > H200000442 H200005719 H300018350) which I want to map to Ensembl or
> RefSeq.
> > I am sure R has a function to do that. I downloaded the {oligo} p...
2012 Mar 19
1
hgu133plus2hsentrezgprobe library
Hello R community,
I am processing raw Affymetrix CEL files and I am using the Michigan custom
CDF library hgu133plus2hsentrezgprobe. I have been looking for
documentation on the function that it contains...I am specifically
interested in converting probe names to gene symbols. Does anybody know
where I can find it?
Thank a lot!
Eleni
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2008 May 06
1
Significance analysis of Microarrays (SAM)
Dear list,
I am trying to perform a significance analysis of a microarray experiment
with survival data using the {samr} package. I have a matrix containing my
data which has 17816 rows corresponding to genes, and 286 columns
corresponding to samples. The name of this matrix is data.matrix2. Some of
the first values of this matrix are:
data.matrix2[1:3,1:5]
GSM36777 GSM36778 GSM36779
2007 Nov 21
4
NA values
Hi all!
I am new to R and I would like to ask you the following question:How
can I substitute the NA values with 0 in a data frame? I cannot find a
command to check if a value is NA...
Thank you very much!
Eleni
2008 Jan 22
4
select repositories under linux
Hi all,
I am trying to install the package "GEOquery" in unix. I have downloaded the
standard version of R and this package is not contained in the default. I
know that I can select repositories under windows but I don't know how to do
it in unix. Does anyone have any idea on this?
Thank you in advance,
Eleni
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2008 Jan 31
3
Memory problem?
Hello R users,
I am trying to run a cox model for the prediction of relapse of 80 cancer
tumors, taking into account the expression of 17000 genes. The data are
large and I retrieve an error:
"Cannot allocate vector of 2.4 Mb". I increase the memory.limit to 4000
(which is the largest supported by my computer) but I still retrieve the
error because of other big variables that I have in
2009 Oct 26
2
help with linear model
Dear list,
I have been searching for a week to fit a simple linear model to my data. I
have looked into the previous posts but I haven't found anything relevant to
my problem. I guess it is something simple...I just cannot see it.
I have the following data frame, named "data", which is a subset of a
microarray experiment. The columns are the samples and the rows are the
probes. I
2007 Nov 23
0
R users in Cyprus
...man/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
------------------------------
Message: 2
Date: Wed, 21 Nov 2007 13:15:32 +0200
From: "Eleni Christodoulou" <elenichri at gmail.com>
Subject: [R] NA values
To: "r-help at r-project.org" <r-help at r-project.org>
Message-ID:
<2293b7660711210315k3c7f1a83v1ed7ff2d3f161adb at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Hi all!
I am new to R and I would like to ask you the...
2008 Jun 06
6
Subsetting to unique values
I want to take the first row of each unique ID value from a data frame.
For instance
> ddTable <-
data.frame(Id=c(1,1,2,2),name=c("Paul","Joe","Bob","Larry"))
I want a dataset that is
Id Name
1 Paul
2 Bob
> unique(ddTable)
Will give me all 4 rows, and
> unique(ddTable$Id)
Will give me c(1,2), but not accompanied by the name column.
2008 Jan 21
1
Help with coxph object
Hello R community!
I am trying to apply the cox model and thus I am creating a coxph object. I
would like to retrieve the p-values from this and keep them separately in
another vector. I can see them when I give a command for the result to
appear. However, the p values are not in the list of values of a coxph
object and I don't know how to keep them for future reference. Could anybody
help me
2008 Feb 19
0
Van't Veer paper on breast cancer
Hello all,
I am working at the FORTH institute in Crete and it's been a long now that I
am trying to reproduce the results of the paper :
"Gene expression profiling predits clinical outcome of breast cancer", by
Van't Veer et al. It has been published in NATURE, vol 415,
31 January 2002.
http://www.nature.com/nature/journal/v415/n6871/full/415530a.html
I am facing some
2008 Mar 03
1
Cox model+ROCR
Dear list,
I am trying to build a cox model and then perform ROC analysis in order to
retrieve some genes that are correlated with breast cancer. When I calculate
the hazard score taking into account different numbers of genes and their
coefficients ( I am trying to find the pest predictor number of genes), I
retrieve from around 1 values (for few genes included ) to size of e+80
values (for many
2008 Mar 19
1
ROC analysis
Hello list,
I am trying to perform ROC analysis and count the AUC in order to validate
my results. I use package ROCR. I would like to count the AUC not under the
cutoff found by "performance" but to use another cutoff that I calculate.
How could I change the following command in order to get what I want?
perform=performance(pred,measure="auc",x.measure="cutoff"),