On Tue, Dec 15, 2009 at 2:34 PM, Peng Yu wrote:
> 2009/12/15 :
>> On Wed, 16 Dec 2009, Peng Yu wrote:
>>
>>> On Tue, Dec 15, 2009 at 10:32 PM, hadley wickham
>>> wrote:
>>>>>
>>>>> I don't understand what these addresses mean.
Currently, I load the RData file then ls() and str(). But loading the file
takes too long if the file is big. Most of the time, I only interested what
the variables are in the the file and the attributes of the variables (like
if it is a data.frame, matrix, what are the colnames/rownames, etc.)
I'
On Thu, Dec 17, 2009 at 5:33 AM, Gustaf Rydevik
wrote:
> On Wed, Dec 16, 2009 at 10:13 PM, Peng Yu wrote:
>>
>> Currently, I load the RData file then ls() and str(). But loading the file
>> takes too long if the file is big. Most of the time, I only interested what
>&g
On Sat, Dec 19, 2009 at 3:35 AM, Patrick Connolly
wrote:
> On Thu, 17-Dec-2009 at 03:13PM +1800, Peng Yu wrote:
>
> |> Currently, I load the RData file then ls() and str(). But loading the file
> |> takes too long if the file is big. Most of the time, I only interested what
>
Suppose that I 'library()' a package, in the 'NAMESPACE' file of the
package, it export some functions to the global namespace. Is there a
way to 'library()' the package without export the functions in
'NAMESPACE' to the global namespace?
__
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On Fri, Dec 18, 2009 at 3:33 AM, Gustaf Rydevik
wrote:
> On Thu, Dec 17, 2009 at 4:33 PM, Peng Yu wrote:
>> On Thu, Dec 17, 2009 at 5:33 AM, Gustaf Rydevik
>> wrote:
>>> On Wed, Dec 16, 2009 at 10:13 PM, Peng Yu wrote:
>>>>
>>>> Currently, I load
I don't find a function to print a string to file. Would somebody let
me know what function I should use?
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I only want to load a limited number of rows by dbReadTable(). I don't
see an option in the help. Is there an option to do so?
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, Benilton Carvalho wrote:
> pm(data)
>
> b
>
> On Dec 26, 2009, at 2:21 PM, Peng Yu wrote:
>
>> I use the following code to do RMA. I'm wondering how get the probe
>> level values before the summary to the probeset level values.
>>
>> library(oligo
ear Peng Yu
>
> how big is the RAM of your computer? You could try with closing all other
> applications before running this script. You could try on a server with more
> RAM.
>
> I tried downloading the file whose URL who give below, but gave up after
> some failed rounds with the
I don't see where describes the implementation of '[]'.
For example, if x is a matrix or a data.frame, how the lookup of
'colname1' is x[, 'colname1'] executed. Does R perform a lookup in the
a hash of the colnames? Is the reference O(1) or O(n), where n is the
second dim of x?
__
z")]
Thank you!
But this is not what I'm asking. I want to know how R internal resolve
which columns to use if I specify the column names rather than the
indexes. If R does it by search, the access time should be O(log(n))
where n is the number of columns. If R does it by hash, the
read.table terminates the program if the input file is empty. Is there
way to let the program continue and return me a NULL instead of
terminating the program?
$ Rscript read_empty.R
> read.table("empty_data.txt")
Error in read.table("empty_data.txt") : no lines available in input
Execution halted
] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> /Henrik
>
> On Fri, Jan 1, 2010 at 12:41 PM, Peng Yu wrote:
>>
> g=try(read.table("data.txt"))
> print(g)
V1 V2 V3 V4
1 name title1 title2 title3
2 row1 10.1 20.1 30.1
3 row2 12.1 22.1 32.1
>
> On Fri, Jan 1, 2010 at 12:41 PM, Peng Yu wrote:
>> read.table terminates the program if the input file is e
Fri, Jan 1, 2010 at 3:55 PM, Ted Harding
> wrote:
>>
>> On 01-Jan-10 20:41:52, Peng Yu wrote:
>> > read.table terminates the program if the input file is empty. Is there
>> > way to let the program continue and return me a NULL instead of
>> > terminating the
On Fri, Jan 1, 2010 at 3:19 PM, Peng Yu wrote:
> On Fri, Jan 1, 2010 at 2:54 PM, Dylan Beaudette
> wrote:
>> ?try
>
> This works. Thank you!
>
>> f=try(read.table("empty_data.txt"))
> Error in read.table("empty_data.txt") : no lines availa
I don't find where in the R document the discussion of nested
namespace is. If there is nested namespace supported in R, could
somebody let me know whether the document is?
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On Thu, Jan 7, 2010 at 11:10 AM, Peng Yu wrote:
> I don't find where in the R document the discussion of nested
> namespace is. If there is nested namespace supported in R, could
> somebody let me know whether the document is?
Could somebody let me know if there is nested name s
I got the following warnings when I install R.oo. Are these warnings
normal? Should I reinstall the package as mentioned in the warnings?
How to reinstall? The sessionInfo() is at the end.
> install.packages("R.oo", dependencies=T)
Warning in install.packages("R.oo", dependencies = T) :
argum
Apparently, Bengtsson.pdf is not current any more. For example, the
installation method is outdated. R.oo.pdf is a reference manual rather
than a tutorial. I'm wondering if there is a better and more current
R.oo tutorial so that I can quickly get started on R.oo.
_
R-lang.pdf has the following description in Section 3.1.1.
"""
Any number typed directly at the prompt is a constant and is evaluated.
> 1
[1] 1
Perhaps unexpectedly, the number returned from the expression 1 is a
numeric. In most
cases, the difference between an integer and a numeric value will b
According to R-lang.pdf (Section 2):
Function mode gives information about the mode of an object in the
sense of Becker,
Chambers & Wilks (1988), and is more compatible with other
implementations of the S
language. Finally, the function storage.mode returns the storage mode
of its argument
in the
I don't find a tutorial on S3. "Bengtsson.pdf" cites MASS (1999
edition). However, I don't think that MASS (2002 edition) clearly
explain what S3 is and help a user who knew very little about S3 to
quickly understand it. Could somebody let me know if there are some
better learning materials to help
On Wed, Jan 20, 2010 at 5:04 PM, Peng Yu wrote:
> I don't find a tutorial on S3. "Bengtsson.pdf" cites MASS (1999
> edition). However, I don't think that MASS (2002 edition) clearly
> explain what S3 is and help a user who knew very little about S3 to
> quickly u
On Wed, Jan 20, 2010 at 5:30 PM, Steve Lianoglou
wrote:
> Hi,
>
> On Wed, Jan 20, 2010 at 6:05 PM, Peng Yu wrote:
>> On Wed, Jan 20, 2010 at 5:04 PM, Peng Yu wrote:
>>> I don't find a tutorial on S3. "Bengtsson.pdf" cites MASS (1999
>>> edition)
On Thu, Jan 21, 2010 at 9:07 AM, Giovanni Petris wrote:
>
> I have found a good refernce to be "S Programming" by Venables and
> Ripley.
I'll take a look at this book.
Since S and R are not completely the same, there are delicate
differences between S and R, which an S book may be confusing if I
I found this paper on ANOVA on unequal error variance. Has this be
incorporated to any R package? Is there any textbook that discuss the
problem of ANOVA on unequal error variance in general?
http://www.jstor.org/stable/2532947?cookieSet=1
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ost
introductory material that I should start with, if I want to
understand the method?
Do you have any simple explanation that may help me understand what is
the difference between the method in 'Exact Statistical Methods for
Data Analysis' and the method in gls()?
> HTH,
> De
On Thu, Jan 21, 2010 at 2:41 PM, Dennis Murphy wrote:
> Hi:
>
> On Thu, Jan 21, 2010 at 12:29 PM, Peng Yu wrote:
>>
>> On Thu, Jan 21, 2010 at 2:16 PM, Dennis Murphy wrote:
>> > Hi:
>> >
>> > This paper was a prelude to his first book '
Please see the following example. I can not write '"' to a csv file
successfully. Could somebody let me if it is possible to write '"' to
a csv file with the default setting of write.csv?
my_home$ Rscript main_quote.R
> x=rbind(
+ "\"A\""
+ , "\"B\""
+ )
> x
[,1]
[1,] "\"A\""
[2,] "\"B\
e quote=T.
I have looking for a way so that the resulted csv file can be read by excel.
http://www.creativyst.com/Doc/Articles/CSV/CSV01.htm#FileFormat
> On Thu, Jan 21, 2010 at 6:29 PM, Peng Yu wrote:
>>
>> Please see the following example. I can not write '"' to
On Fri, Jan 22, 2010 at 3:33 PM, Dennis Murphy wrote:
> Hi:
>
> On Thu, Jan 21, 2010 at 1:06 PM, Peng Yu wrote:
>>
>> On Thu, Jan 21, 2010 at 2:41 PM, Dennis Murphy wrote:
>> > Hi:
>> >
>> > On Thu, Jan 21, 2010 at 12:29 PM, Peng Yu wrote:
>
I'm wondering if there is a way to make blocks of code independent
from each other. Please see the following example for what I mean.
x=1
## is there a way to make the following assignment not affect the above x?
## in C++, I can use {} to make the effect local. Is there an
equivalent construct i
By default, my R functions run silently if NA is encountered? I would
like them to give me some message when NA is encountered by default.
Note that I could check each intermediate variable by something like
is.na(). But this is not manageable for big programs, so I'd like a
way to check NA global
Could somebody recommend some good nonparametric statistical inference
textbooks for a beginner? And what are pros and cons of each book?
Nonparametric statistical methods by Hollander seems to be more
difficult for a beginner, but is great as a reference, right? Are
there any books that are easie
On Mon, Oct 19, 2009 at 12:53 PM, Kingsford Jones
wrote:
>> sum((x-mean(x))^2)/(n)
> [1] 0.4894708
>> ((n-1)/n) * var(x)
> [1] 0.4894708
But this is not a built-in function in R to do so, right?
> hth,
> Kingsford
>
> On Mon, Oct 19, 2009 at 9:30 AM, Peng Y
?contrast in the contrast package gives me the following description.
However, I have no idea what Type II and III contrasts are. Could
somebody explain it to me? And what does 'type' mean here?
*‘type’*: set ‘type="average"’ to average the individual contrasts
(e.g., to obtain a Type II o
It seems that Eq (2) in the vignettes for the 'contrast' packages is
not correct. That is, the numerator on the right hand side should be
$c' \beta$ rather than $c' \lambda$, right? If I'm correct, could
somebody notice the author to fix it?
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> library(contrast)
> contrast
function (fit, ...)
UseMethod("contrast")
I guess the above function is S3. Could somebody let me know how to
show the function body in an R session?
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contrast.geese contrast.glscontrast.lm
[5] contrast.lme
> methods("contrast.lm")
no methods were found
Warning message:
In methods("contrast.lm") :
function 'contrast.lm' appears not to be generic
> contrast.lm
function (fit, ...)
contrastCalc(fit, ...)
I read the vignette of contrast package. I don't think that I
understand how to use it.
I made the following simpler example (contrast between '3' and '4').
Could somebody let me know what is the correct way to compute the
contrast in the following example?
library(contrast)
a=3
n=4
A = as.v
On Tue, Feb 2, 2010 at 11:04 PM, David Winsemius wrote:
>
> On Feb 2, 2010, at 11:42 PM, Peng Yu wrote:
>
>> It seems that Eq (2) in the vignettes for the 'contrast' packages is
>> not correct. That is, the numerator on the right hand side should be
>> $c&#x
On Tue, Feb 2, 2010 at 11:14 PM, David Winsemius wrote:
>
> On Feb 3, 2010, at 12:11 AM, Peng Yu wrote:
>
>> On Tue, Feb 2, 2010 at 11:04 PM, David Winsemius
>> wrote:
>>>
>>> On Feb 2, 2010, at 11:42 PM, Peng Yu wrote:
>>>
>>>> It se
On Tue, Feb 2, 2010 at 11:22 PM, David Winsemius wrote:
>
> On Feb 3, 2010, at 12:20 AM, Peng Yu wrote:
>
>> On Tue, Feb 2, 2010 at 11:14 PM, David Winsemius
>> wrote:
>>>
>>> On Feb 3, 2010, at 12:11 AM, Peng Yu wrote:
>>>
>>>> On Tu
On Wed, Feb 3, 2010 at 2:12 AM, Emmanuel Charpentier
wrote:
> Le mercredi 03 février 2010 à 00:01 -0500, David Winsemius a écrit :
>> On Feb 2, 2010, at 11:38 PM, Peng Yu wrote:
>>
>> > ?contrast in the contrast package gives me the following description.
>> > How
On Wed, Feb 3, 2010 at 8:41 AM, David Winsemius wrote:
>
> On Feb 3, 2010, at 9:28 AM, Peng Yu wrote:
>
>> On Tue, Feb 2, 2010 at 11:22 PM, David Winsemius
>> wrote:
>>>
>>> On Feb 3, 2010, at 12:20 AM, Peng Yu wrote:
>>>
>>>> On Tu
On Wed, Feb 3, 2010 at 10:01 AM, Peng Yu wrote:
> Some examples in the help page are too long to be copied from screen.
> Could somebody let me know some easy way on how to extract the example
> to a file so that I can play with them?
I forget to mention. I use a terminal ver
Some examples in the help page are too long to be copied from screen.
Could somebody let me know some easy way on how to extract the example
to a file so that I can play with them?
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Suppose that I have the following list of lists of frames 'root'
(let's call it a 'tree' of frames). I want to flatten it to be a list
of frames. However, if I unlist(root), it will flatten the frames as
well. Is there a simply way to flatten the tree to certain depth?
aframe1=data.frame(x=1:3,y=1
On Wed, Feb 3, 2010 at 12:29 PM, Steve Lianoglou
wrote:
> Hi,
>
> On Wed, Feb 3, 2010 at 1:19 PM, Peng Yu wrote:
>> Suppose that I have the following list of lists of frames 'root'
>> (let's call it a 'tree' of frames). I want to flatten it to be
.
> -Original Message-
> From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
> Behalf Of Peng Yu
> Sent: Wednesday, February 03, 2010 10:20 AM
> To: r-h...@stat.math.ethz.ch
> Subject: [R] How to flatten a tree (based on list) to a certain depth?
>
>
-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
> Behalf Of Peng Yu
> Sent: Wednesday, February 03, 2010 11:40 AM
> To: r-h...@stat.math.ethz.ch
> Subject: Re: [R] How to flatten a tree (based on list) to a certain depth?
>
> On Wed, Feb 3, 2010 at 12:26 PM, Bert Gunt
Hi Chad,
There are not many significant transcript clusters after p.adjust.
> sum(adjusted_pvalue[,'C-D']<.05)
[1] 0
> sum(adjusted_pvalue[,'A-D']<.05)
[1] 0
> sum(adjusted_pvalue[,'D-E']<.05)
[1] 2
> sum(adjusted_pvalue[,'A-B']<.05)
[1] 8
However, there are may TCs that are significant before p
On Wed, Feb 3, 2010 at 3:48 PM, Max Kuhn wrote:
> Wait, what were we talking about? Right...it is a typo. It should be
> c'beta in the numerator.
>
> Peng: As the package maintainer, you really should send me a quick
> email about it instead of posting to the list.
>
> Let's not waste the bandwidt
pe...@morgan:~/projects/APP_Hippo_Exon_Jankowsky/analysis/pvalue_contrast_table.RData
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and provi
On Wed, Feb 3, 2010 at 4:53 PM, David Scott wrote:
> Peng Yu wrote:
>>
>> On Wed, Feb 3, 2010 at 3:48 PM, Max Kuhn wrote:
>>>
>>> Wait, what were we talking about? Right...it is a typo. It should be
>>> c'beta in the numerator.
>>>
>>
bcp()'s help says it implements the paper by Barry and Hartigan
(1993). But it has 4 other citations which are later than 1993. Could
somebody who have experience on this function let me know why these 4
later citations matters to this particular function? Or these
citations are just for the topic
iki/Variance#Population_variance_and_sample_variance.
After all, many none pure statisticians relies on wiki for easy access
of some simple terms.
>> -Original Message-
>> From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
>> project.org] On Behalf Of Ista Zahn
On Thu, Feb 4, 2010 at 4:34 PM, Henrik Bengtsson wrote:
> On Thu, Feb 4, 2010 at 9:18 PM, Liaw, Andy wrote:
>> From: Peng Yu
>>>
>>> On Wed, Feb 3, 2010 at 10:01 AM, Peng Yu wrote:
>>> > Some examples in the help page are too long to be copied
>>&g
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