Displaying 20 results from an estimated 8000 matches similar to: "NA values"
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 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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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
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 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
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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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 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 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 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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2007 Sep 14
6
replace NA value with 0
Hi,
how can I replace NA value with 0:
1991 217 119 103 109 137 202 283 240 146 NA
1992 270 174 149 144 166 239 278 237 275 NA
1993 146 111 104 89 98 131 153 148 175 NA
1994 177 123 146 124 121 200 266 191 240 106
1995 145 98 95 89 95 130 183 161 164 129
1996 145 98 89 90 93 138 158 131 161 161
1991 217 119 103 109 137 202 283 240 146 0
1992 270 174 149 144 166 239 278 237
2007 Nov 28
2
Clustering
Hello all!
I am performingsome clustering analysis on microarray data using
agnes{cluster} and I have created my own dissimilarity matrix according to a
distance measure different from "euclidean" or "manhattan" etc. My question
is, if I choose for example method="complete", how are the distances
between the elements calculated? Are they taken form the dissimilarity
2009 Dec 02
1
Ridge regression
Dear list,
I have a couple of questions concerning ridge regression. I am using the
lm.ridge(...) function in order to fit a model to my microarray data.
Thus *model=lm.ridge(...)*
I retrieve some coefficients and some scales for each gene. First of all, I
would like to ask: the real coefficients of the model are not included in
the first argument of the output but in the result of coef(model),
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
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"),
2009 Dec 11
1
SVM regression
Dear R users,
I am trying to apply SVM regression for a set of microarray data. I am using
the function svm() under the package {e1071}. Can anyone tell me what
the *residuals
*value represents? I have some observed values *y_obs* for the parameter
that I want to estimate and I would expect that *svm$residuals = y_obs -
svm$fitted.
*However, this does not happen...Does anyone have any idea on
2010 Mar 04
1
sum of list elements
Dear list,
I have some difficulty in manipulating list elements. More specifically, I
am performing svm regression and have a list of lists, called pred.svm. The
elements of the second list are 3D arrays. Thus I have pred.svm[[i]][[j]],
with 1<=i<=5 and 1<=j<=20.
I want to take the sum of the elements a specific array dimension across all
j, for one i. Mathematically speaking, I want
2008 Feb 14
5
Removing columns that are all NA from a matrix
Hi,
I guess this might be a FAQ or something, and there's probably a nice
simple way to do it, but I can't think of it:
Given a matrix, I want to remove columns that are _entirely_ filled with
NAs (partial NAs are fine).
How please?
Thanks,
Martin
2008 Jun 02
2
request: To add an extra row in a matrix
Dear R users
I have a problem regarding an addition of an extra "row" to a matrix. e.g. i have a matrix
a <- matrix(1:6,2,3)
> a
[,1] [,2] [,3]
[1,] 1 3 5
[2,] 2 4 6
I want to add a matrix having just one row. e.g.
b <- matrix(7:9,1,3)
> b
[,1] [,2] [,3]
[1,] 7 8 9
Now i want to get result like this
[,1] [,2] [,3]
[1,] 1 3 5