Hi,
I'm trying to build a Forest Plot using the second and fourth columns in
the table (test.csv) below. My code is the following:
curated <- data.frame("test.csv")
tmp <- curated$coef
tmp1 <- curated$se_coef
plt <- metaplot(tmp, tmp1, xlim = c(-.45, .45))
I keep getting the following error at th
Hey,
I just googled my error and many things came up. I followed the leads and
read the ?read.delim page; I tried changing header = TRUE, and row.names =
TRUE-- but I've still been having trouble fixing it, so I would greatly
appreciate any help you can provide. Here is my code:
rm(list=ls())
s
ihui.name
>> Department of Statistics, Iowa State University
>> 2215 Snedecor Hall, Ames, IA
>>
>>
>>
>> On Wed, Feb 15, 2012 at 4:09 PM, Ben Ganzfried
>> wrote:
>>
>>> Hi Martin,
>>>
>>> Thanks! You were right. Quotes see
on
would be really greatly appreciated!
Thanks!
Ben
On Wed, Feb 15, 2012 at 4:20 PM, Martin Morgan wrote:
> On 02/15/2012 12:18 PM, Ben Ganzfried wrote:
>
>> Hey,
>>
>> I keep getting the following warning:
>>
>> data(GSE19829-GPL570_eset)
>>>
>
Hey,
I keep getting the following warning:
> data(GSE19829-GPL570_eset)
Warning in data(GSE19829 - GPL570_eset) :
data set GSE19829 - GPL570_eset not found
> ## maybe str(GSE19829-GPL570_eset) ; plot(GSE19829-GPL570_eset) ...
>
> if(require(affy)){
+ summary(GSE19829-GPL570_eset$vital_statu
atinum resistance:
refractory=death in 6mo or less, sensitive=survival for 12mo or more.
For "debulking": amount of residual disease (optimal = <1mm,
suboptimal=>1mm).
}
2012/2/8 Uwe Ligges
>
>
> On 08.02.2012 18:44, Ben Ganzfried wrote:
>
>> Hi--
&g
Hi--
I googled the above error and found previous postings about this error on
the list. I was having a little difficulty implementing the advice though.
The suggestions were to use: traceback() and checkRd(). I'm using R in
the directory in which the .Rd file with the problem is located, but I
Hi,
I'm just finishing up an R package and I was wondering if anyone knows how
to include institution name in the "Description File." That is, my current
Description File looks like:
Package: curatedCancerData
Type: Package
Title: Cancer Gene Expression Analysis
Version: 1.0
Date: 2011-12-24
Aut
7:12 PM, Duncan Murdoch wrote:
> On 11-12-16 4:12 PM, Ben Ganzfried wrote:
>
>> Hi--
>>
>> I'm creating an R package, I've read through "Writing R Extensions" and
>> the
>> package.skeleton() R page-- and I'm still running into
*the line in question is*:
> package.skeleton(name = "a", code_files = "EsetObject.r")
On Fri, Dec 16, 2011 at 4:12 PM, Ben Ganzfried <
benganzfr...@post.harvard.edu> wrote:
> Hi--
>
> I'm creating an R package, I've read through "Writing R
Hi--
I'm creating an R package, I've read through "Writing R Extensions" and the
package.skeleton() R page-- and I'm still running into a little confusion.
I would greatly appreciate any advice you can provide.
Where do I run my following line of code from?:
> package.skeleton(name = "a", code_fi
Thanks!
On Fri, Oct 28, 2011 at 10:59 AM, Marc Schwartz wrote:
> On Oct 28, 2011, at 9:49 AM, Ben Ganzfried wrote:
>
> > Hey,
> >
> > I'm trying to match patient identifiers from two separate input files,
> and
> > then add information from one of the inp
Hey,
I'm trying to match patient identifiers from two separate input files, and
then add information from one of the input files to the corresponding output
file. I'd greatly appreciate any help!
More specifically,
Input_File_1 has a column header "bcr_patient_barcode"
Input_File_2 has a column
se ask on the
> Bioconductor mailing list. Good news, you don't have to subscribe to post
>
> http://bioconductor.org/help/**mailing-list/<http://bioconductor.org/help/mailing-list/>
>
> Martin
>
>
> On 10/07/2011 07:27 AM, Ben Ganzfried wrote:
>
>> Hey,
>>
Hey,
I have code that can check the quality of a data set we're working with
(expression data), and I'm having some trouble writing code that would make
the expression data we have tie to other data we want to link it to (called
phenotype data). Does anyone have any advice on how I could make a s
wrote:
>
>
>> On Sep 16, 2011, at 10:36 AM, Ben Ganzfried wrote:
>>
>> Hi guys,
>>>
>>> snipped
>
>
>>> Second, I changed the first line of my code to:
>>> tmp <-
>>> ifelse(uncurated$days_to_**tumor_recurrence==NA,&qu
If that's the case, you need to write is.null(),
> something like is.NA()...
>
> Michael Weylandt
>
> On Fri, Sep 16, 2011 at 10:36 AM, Ben Ganzfried
> wrote:
>
>> Hi guys,
>>
>> My code (next 2 lines below) isn't doing what I'm expectin
Hi guys,
My code (next 2 lines below) isn't doing what I'm expecting it to:
tmp <-
ifelse(uncurated$days_to_tumor_recurrence=="null","norecurrence","recurrence")
curated$recurrence_status <- tmp
I want the column "recurrence_status" in my output file to have values
"recurrence" (if the input val
t;
> > a <- "b"
> > z <- data.frame(a=1:3, b=4:6)
> > z[ ,"a"] # the "a" column of z
> > z[ ,a] # the column of z with the value of the object a
> >
> > HTH,
> >
> > -- Bert
> >
> >
> > On Mon, Ju
not think the as.character is needed. Coercion to character is
> implicit in the use of paste(). And the sep argument could be "+".
>
> output = paste(df [,'Major.Gleason'], df[ ,'Minor.Gleason'], sep='+')
>
> --
> David.
>
>
>
>
Hi --
I had a pretty quick R question since unfortunately I have not been able to
find an answer on Google. It shouldn't take much more than a minute to
answer.
I'm trying to add up the major gleason grade and minor gleason grade for an
analysis of patients with prostate cancer. One column has
Hi--
I'm trying to teach myself R using Peter Dalgaard's "Introductory Statistics
with R." Does anyone know if there are solutions available for the
exercises?
I'm really just hoping to learn by going through exercises and checking
myself, so alternatively, does anyone know of an introductory te
I'm looking over good-code a post-doc in my lab wrote and trying to learn
how it works. I came across the following:
rel.abundance <- as.matrix(read.delim("rel.abundance.csv",row.names=1,as.is
=TRUE))
rel.abundance <- log2(rel.abundance-min(rel.abundance)+1)
I'm not sure what the second line is d
nto the more important and interesting parts of
the study. I really appreciate all your suggestions and help.
Sincerely,
Ben
On Tue, Jun 7, 2011 at 12:53 PM, Duncan Murdoch wrote:
> On 07/06/2011 12:41 PM, Ben Ganzfried wrote:
>
>> Hi,
>>
>> My project is set up the follo
Hi,
My project is set up the following way:
root directory contains the following folders:
folders: "Breast_Cancer" AND "Colorectal_Cancer" AND "Lung_Cancer" AND
"Prostate_Cancer"
I want to create a file, call it: "repeating_functions.R" and place it in
the root directory such that I can call t
ubtedly face similar but different situations many times in the future
and I want to make sure that I know how to solve them.
Thanks again--I really appreciate your kindness.
Ben Ganzfried
On Thu, Jun 2, 2011 at 3:33 PM, David Winsemius wrote:
>
> On Jun 2, 2011, at 2:54 PM, Ben Ganzfried wrot
element to the right of "N". I've read the
regular expression tutorial for R, but could only figure out how to grab an
integer value if it is the only integer value in the row (ie more than one
integer value makes this basic regular expression unsuccessful).
Thank you very much for
27 matches
Mail list logo
