[R] How to prepare a input data for Cytoscape

[Elham - via R-help]

Hello,I want to use "Cytoscape"  to construct co-expression network for 
coding-lncoding (control/tretment situation).I calculated correlation by R for 
control and treatment and now I want to prepare input data for cytoscape, 
I want molecules (genes and lncRNA) as nodes andcorrelation weighting the edges 
connecting them,also use value of correlation as an Edge weights too.should I  
prepare input table with 6 column? 1-coding genes 2-lncoding 3-pairs of 
treatment 4-pairs of control 5-value of treatment correlation 6-value of 
control correlationthat first and second are nodes and others are edges?
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Re: [R] filter correlation data

[Elham - via R-help]

actually,First I searched in net,after that I sent my question, because I 
couldn't find the function. 

On Wednesday, February 1, 2017 1:34 AM, Bert Gunter 
<bgunter.4...@gmail.com> wrote:
 

 ... And why did you not do a web search on "correlation coefficient in
R", which would have led you almost imediately to ?cor and friends?

-- Bert


Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Tue, Jan 31, 2017 at 1:34 PM, Elham - via R-help
<r-help@r-project.org> wrote:
> hello everybody,I have a very very huge table in R from calculating 
> correlation,how can I filter it per spearman correlation and p-value before 
> export it,I mean what is the function that I use?I want to select the pairs 
> for value (r), , greater than 0.9 (directly correlated) and less than -0.9 
> (inversely corerlated), and a p-value < 0.001
>
>
> I should say that I transformed the big matrix in a table by library(reshape).
>        [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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> and provide commented, minimal, self-contained, reproducible code.

   
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[R] filter correlation data

[Elham - via R-help]

hello everybody,I have a very very huge table in R from calculating 
correlation,how can I filter it per spearman correlation and p-value before 
export it,I mean what is the function that I use?I want to select the pairs for 
value (r), , greater than 0.9 (directly correlated) and less than -0.9 
(inversely corerlated), and a p-value < 0.001


I should say that I transformed the big matrix in a table by library(reshape).
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Re: [R] caculate correlation

[Elham - via R-help]

this script automatically recognizes what is control among cod and lnc. Note 
that this script contains a piece of text that is "grep(".C",cod$name)". This 
text select - among all column names - those that contain ".C". in my files, I 
named C1, C2, C3, etc all columns that correspond to controls. In the same 
manner, I get controls among the lnc, with the text: "grep(".C",lnc$name)"
I`m so sorry,maybe I do not understand you again.

On Tuesday, January 31, 2017 1:27 AM, Jim Lemon <drjimle...@gmail.com> 
wrote:
 

 Hi Elham,
This is about the same as your first message. What I meant was, what
do these two expressions return? Is whatever is returned suitable
input for the "cor" function?

coding.rpkm[grep("23.C",coding.rpkm$name),-1]

ncoding.rpkm[grep("23.C",ncoding.rpkm$name),-1]

Jim


On Tue, Jan 31, 2017 at 8:45 AM, Elham - <ed_isfah...@yahoo.com> wrote:
> I have 9 experiments control/treatment that I analysed coding and lncoding,
> after that I normalize expression value.as you know we have different known
> number of coding and non -coding genes,so for calculating correlation first
> I transposed data ,(rows become columns)so row is control and
> columns are gene names.(so I have 2 matrix with same row and different
> column).This information is enough?
>
>
>
>
> On Tuesday, January 31, 2017 1:06 AM, Jim Lemon <drjimle...@gmail.com>
> wrote:
>
>
> Hi Elham,
> Without knowing much about what coding.rpkm and ncoding.rkpm look
> like, it is difficult to say. Have you tried to subset these matrices
> as you do in the "cor" function and see what is returned?
>
> Jim
>
> On Tue, Jan 31, 2017 at 6:40 AM, Elham - via R-help
> <r-help@r-project.org> wrote:
>> for calculating correlation between coding and noncoding,first I
>> transposed data ,(rows become columns) so row is control and
>> columns are gene names.(so I have 2 matrix with same row and different
>> column),I use these function for calculating correlation but all of spearman
>> correlation are NA,why?
>>
>>
>>
>> control.corr=cor(coding.rpkm[grep("23.C",coding.rpkm$name),-1],ncoding.rpkm[grep("23.C",ncoding.rpkm$name),-1],method=
>> "spearman")
>>
>>
>>
>>
>>
>>
>>
>> tumor.corr=cor(coding.rpkm [grep("27.T", coding.rpkm $name),-1],
>> ncoding.rpkm [grep("27.T", ncoding.rpkm $name),-1],method = "spearman")
>>
>>        [[alternative HTML version deleted]]
>>
>> __
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/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.
>
>


   
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Re: [R] caculate correlation

[Elham - via R-help]

I have 9 experiments control/treatment that I analysed coding and lncoding, 
after that I normalize expression value.as you know we have different known 
number of coding and non -coding genes,so for calculating correlation first I 
transposed data ,(rows become columns)so row is control and columns 
are gene names.(so I have 2 matrix with same row and different column).This 
information is enough?  
 

On Tuesday, January 31, 2017 1:06 AM, Jim Lemon <drjimle...@gmail.com> 
wrote:
 

 Hi Elham,
Without knowing much about what coding.rpkm and ncoding.rkpm look
like, it is difficult to say. Have you tried to subset these matrices
as you do in the "cor" function and see what is returned?

Jim

On Tue, Jan 31, 2017 at 6:40 AM, Elham - via R-help
<r-help@r-project.org> wrote:
> for calculating correlation between coding and noncoding,first I transposed 
> data ,(rows become columns) so row is control and columns are gene 
> names.(so I have 2 matrix with same row and different column),I use these 
> function for calculating correlation but all of spearman correlation are 
> NA,why?
>
>
> control.corr=cor(coding.rpkm[grep("23.C",coding.rpkm$name),-1],ncoding.rpkm[grep("23.C",ncoding.rpkm$name),-1],method=
>  "spearman")
>
>
>
>
>
>
>
> tumor.corr=cor(coding.rpkm [grep("27.T", coding.rpkm $name),-1], ncoding.rpkm 
> [grep("27.T", ncoding.rpkm $name),-1],method = "spearman")
>
>        [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/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.

   
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[R] caculate correlation

[Elham - via R-help]

for calculating correlation between coding and noncoding,first I transposed 
data ,(rows become columns) so row is control and columns are gene 
names.(so I have 2 matrix with same row and different column),I use these 
function for calculating correlation but all of spearman correlation are NA,why?


control.corr=cor(coding.rpkm[grep("23.C",coding.rpkm$name),-1],ncoding.rpkm[grep("23.C",ncoding.rpkm$name),-1],method=
 "spearman")






 
tumor.corr=cor(coding.rpkm [grep("27.T", coding.rpkm $name),-1], ncoding.rpkm 
[grep("27.T", ncoding.rpkm $name),-1],method = "spearman")

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[R] co-expression network of coding-noncoding genes

[Elham - via R-help]

hello all,

I have 9 experiments (human RNAseq data (control/treatment)),I did RNAseq 
analysis by CLC genomics,after normalization I calculated correlation, I have 
many pairs of coding and lncoding molecules that correlate according to their 
expression,I filtered them (> 0.9 and < -0.9). Additionally, I've considered 
the pairs that have p-values < 0.001,but they are many pairs yet.

now for more filtering I want to consider the pairs of coding-non coding, which 
are both deferentially expressed. 
how can I have DE for all treated vs all controls samples for coding and DE for 
all treated vs all controls samples for noncoding?


I should say that each experiment is effect of one drug on one cancer (drugs 
and cancers are different in each experiment ) but the platform is similar and 
all of them are Illumina HiSeq 2000 (Homo sapiens)

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[R] Access GSE Data Tables from GEO by GEOquery

[Elham - via R-help]

hello all,I am following this link 
http://genomicsclass.github.io/book/pages/GEOquery.html for importing data.but 
I have a problem in a step of (Access GSE Data Tables from GEO).in the example 
of tutorial there are 266 samples,but by this function
    


                                                                
 the result in R is:



where is another samples?





























 
   

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[R] GEOquery

[Elham - via R-help]

hello all,I am following this link 
http://genomicsclass.github.io/book/pages/GEOquery.html for importing data.but 
I have a problem in a step of (Access GSE Data Tables from GEO).in the example 
of tutorial there are 266 samples,but by this function
dim(pData(gse[[1]]))head(pData(gse[[1]])[, 1:3])                                
                                            the result in R is:

> dim(pData(gse[[1]]))[1] 266  47> head(pData(gse[[1]])[, 1:3])          title 
> geo_accession                statusGSM540108   BC1     GSM540108 Public on 
> May 05 2010GSM540109   BC2     GSM540109 Public on May 05 2010GSM540110   BC3 
>     GSM540110 Public on May 05 2010GSM540111   BC4     GSM540111 Public on 
> May 05 2010GSM540112   BC5     GSM540112 Public on May 05 2010GSM540113   BC6 
>     GSM540113 Public on May 05 2010
where is another samples? 
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Re: [R] help for

[Elham - via R-help]

yes me too,but I do not have time to install and learn linux,I need tutorial 
based on windows 

On Saturday, December 31, 2016 3:50 AM, David Winsemius 
<dwinsem...@comcast.net> wrote:
 

 
> On Dec 30, 2016, at 9:57 AM, Elham - via R-help <r-help@r-project.org> wrote:
> 
> hi all, I am following 
> http://bioinformatics.knowledgeblog.org/2011/06/20/analysing-microarray-data-in-bioconductor/

That page was designed by and for someone with  Linux installation. To quote 
from the opening paragraph: "Some familiarity with Linux is ideal and the 
instructions were developed on Ubuntu 11.04, R 2.12.1. For a full code listing 
for this tutorial and figures resulting from it see the second part of the 
article."

> I need to download phenotypic data in the form of text file that describe 
> chip names, and the source of the biological samples as well as probe that 
> hybridised to them. I can not understand the mean of "Open a new terminal 
> window and type".
> i am using command.$ ls data/*.CEL > data/phenodata.txt in R
> 
> this returns an error
> 
> 
> $ ls data/*.CEL > data/phenodata.txt Error: unexpected '$' in "$"
> what should I do now?

It later runs out that you are on Windows?   ???

> 
>     [[alternative HTML version deleted]]
> 

There is a help facility for BioC questions. (I think it might now  be 
web-based unlike this mailing list which remains plain text.)  I suggest you 
read the Posting Guide more thoroughly that it appears you have so far.


> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/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.

David Winsemius
Alameda, CA, USA


   
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Re: [R] help for

[Elham - via R-help]

actually I do not work with linux. do you know same of this tutorial for 
windows? 

On Friday, December 30, 2016 10:16 PM, John McKown 
 wrote:
 

 On Fri, Dec 30, 2016 at 12:08 PM, Sarah Goslee  wrote:

This isn't an R question, but a linux question.

Open a new terminal window:
The directions you are following tell you how to do that for the
Ubuntu linux being used, right at the beginning:

Open up a terminal (Applications->Accessories-> Terminal from the the toolbar)

As for your command, the $ is a prompt. You don't type that. Start with ls

What should you do now? Read a little bit about using linux command line tools


​Well, this being the R language forum, perhaps you should enter "R" after the 
command prompt?
Seriously, what do you want to accomplish? Since you are using Ubuntu, I will 
assume that you are using the default shell program, BASH. There is a BASH 
forum you could join called mailto:help-b...@gnu.org . It's easiest to sign up 
here: https://lists.gnu.org/mailman/listinfo/help-bashThis site has some nice 
articles about BASH and programming (scripting) using it: 
http://wiki.bash-hackers.org/BASH for beginners: 
http://www.tldp.org/LDP/Bash-Beginners-Guide/html/Since you seem to be using 
Ubuntu: https://help.ubuntu.com/community/Beginners/BashScripting
There are _TONS_ of commands installed in Ubuntu by default. Most of them have 
manual (man) pages. Most of the defaults are in the directory /usr/bin. You can 
list them simply by entering the command: "ls /usr/bin". My system has over 
6,500 programs stuffed in there. If you see something interesting, you can get 
some basic documentation on it by using the command: "man ". We've 
mentioned "ls", which lists the contents of a directory. If you want to know 
more, try "man ls". In addition to "man" there is a much more powerful 
information source called "info". Just use it instead of "man" as the command 
name. That is, use "info ls" to get some real detailed information on the ls 
command.
Another interesting command is "apropos". Think of it as being similar to the R 
systems' double question mark search. As an example, suppose you want to find 
out what commands might be helpful with a "zip" file. Enter the command: 
"apropos zip". On my system, I get a (truncated) response such as:
bunzip2 (1)          - a block-sorting file compressor, v1.0.6bzip2 (1)         
   - a block-sorting file compressor, v1.0.6
bzip2recover (1)     - recovers data from damaged bzip2 filesbzless (1)         
  - file perusal filter for crt viewing of bzip2 compressed textdecode (n)      
     - Access to zip archives
encode (n)           - Generation of zip archives
funzip (1)           - filter for extracting from a ZIP archive in a pipegunzip 
(1)           - compress or expand files
gzip (1)             - compress or expand filesIO::Compress::Bzip2 (3pm) - 
Write bzip2 files/buffers
IO::Compress::Zip (3pm) - Write zip files/buffers
IO::Uncompress::Unzip (3pm) - Read zip files/buffers
unzip (1)            - list, test and extract compressed files in a ZIP archive
unzipsfx (1)         - self-extracting stub for prepending to ZIP 
archiveszforce (1)           - force a '.gz' extension on all gzip fileszip (1) 
             - package and compress (archive) fileszipcloak (1)         - 
encrypt entries in a zipfile
Note the number in the parentheses after the command. A "1" indicates this is a 
normal command. Something which starts with a "3" (like 3pm) means this is like 
a subroutine package (The "pm" in 3pm means "Perl Module" - like an R package, 
sort of). Also note that some of the entries have nothing to do with a normal 
"zip" file; such as the entires with bzip2 in them - bzip2 is an alternative 
compressor program).

I'm fairly good with BASH, having programmed for over 3 decades, and used BASH 
for about 10 years. Which is both good and bad. The good is that I understand 
BASH fairly well. The bad is that I like "tricky coding" (a personal problem).
 

Sarah



-- 
There’s no obfuscated Perl contest because it’s pointless.

—Jeff Polk
Maranatha! <><
John McKown

   
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[R] help for

[Elham - via R-help]

hi all, I am following 
http://bioinformatics.knowledgeblog.org/2011/06/20/analysing-microarray-data-in-bioconductor/
 I need to download phenotypic data in the form of text file that describe chip 
names, and the source of the biological samples as well as probe that 
hybridised to them. I can not understand the mean of "Open a new terminal 
window and type".
i am using command.$ ls data/*.CEL > data/phenodata.txt in R

this returns an error


$ ls data/*.CEL > data/phenodata.txt Error: unexpected '$' in "$"
what should I do now?

[[alternative HTML version deleted]]

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Re: [R] calculate correlations

[Elham - via R-help]

hello Michael,I specified each column like this screenshot:(A.C1 means 
experiment A and first control,A.T3 means experiment A and third treatment  
 ) I have two transposed file,one for coding and one for lncoding.




 

On Wednesday, December 7, 2016 6:11 PM, Michael Dewey 
<li...@dewey.myzen.co.uk> wrote:
 

 If I understand this correctly you are choosing all the rows from each 
of cod and lnc which contain .c (ie any character followed by a C) and 
deleting the first column from each of cod and lnc. You then correlate 
them so that you get the correlation between corresponding columns of 
each. Since you do not tell us how you know which column is which it is 
hard to answer the question of how R will know.

On 07/12/2016 11:26, Elham - via R-help wrote:
> Hi All,I have 11 human RNA-seq data (control/treatment),The effect of various 
> drugs on various cancers,I want to calculate the genes-lncRna correlations 
> for all tumors considered together for network,I did differential expression 
> analysis and prepared normalized values (rpkm) of coding and lncoding in two 
> separate file and import them to R, then transpose them and now I want to 
> calculate corr by this function:
> control.corr=cor(cod[grep(".C",cod$name),-1],lnc[grep(".C",lnc$name),-1],method
>  = "spearman")
>
> if I understand true,I should write the numbers of columns whose related to 
> control,then I counted all of control`s column and wrote 23 .now my question 
> is,how does R understand what column is control and what is treatment?
>
>
>     [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/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.
>

-- 
Michael
http://www.dewey.myzen.co.uk/home.html


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[R] calculate correlations

[Elham - via R-help]

Hi All,I have 11 human RNA-seq data (control/treatment),The effect of various 
drugs on various cancers,I want to calculate the genes-lncRna correlations for 
all tumors considered together for network,I did differential expression 
analysis and prepared normalized values (rpkm) of coding and lncoding in two 
separate file and import them to R, then transpose them and now I want to 
calculate corr by this function:
control.corr=cor(cod[grep(".C",cod$name),-1],lnc[grep(".C",lnc$name),-1],method 
= "spearman")

if I understand true,I should write the numbers of columns whose related to 
control,then I counted all of control`s column and wrote 23 .now my question 
is,how does R understand what column is control and what is treatment?


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[R] memory allocation problem

[Elham - via R-help]

hi everyone,
I tried to run my code in RStudio,but I received this error message,what should 
I do?
Error: cannot allocate vector of size 12.1 Gb
In addition: Warning messages:
1: In cor(coding.rpkm[grep("23.C", coding.rpkm$name), -1], 
ncoding.rpkm[grep("23.C",  :
  Reached total allocation of 6027Mb: see help(memory.size)
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[R] (no subject)

[Elham - via R-help]

hi everyone,I tried to run my code in RStudio,but I received this error 
message,what should I do?Error: cannot allocate vector of size 12.1 Gb
In addition: Warning messages:
1: In cor(coding.rpkm[grep("23.C", coding.rpkm$name), -1], 
ncoding.rpkm[grep("23.C",  :
  Reached total allocation of 6027Mb: see help(memory.size)

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Re: [R] transpose rows and columns for large data

[Elham - via R-help]

thank you all,it worked 

On Tuesday, November 29, 2016 9:49 PM, "Dalthorp, Daniel" 
<ddalth...@usgs.gov> wrote:
 

 Try David's suggestion to spell the argument "stringsAsFactors" correctly. 
Then:

data <- read.table("your_file_location", sep ="\t", comment.char = "", 
stringsAsFactors = F, header = T)
transpose_data <- t(data)

-Dan
On Tue, Nov 29, 2016 at 9:56 AM, Elham - via R-help <r-help@r-project.org> 
wrote:

yes you have right about excel.by R,what should I do for transposing row and 
column?

    On Tuesday, November 29, 2016 9:13 PM, David Winsemius 
<dwinsem...@comcast.net> wrote:



> On Nov 29, 2016, at 9:22 AM, Elham - via R-help <r-help@r-project.org> wrote:
>
> Hi,
>
> I am trying to transpose large datasets inexcel (44 columns and 57774 rows) 
> but it keeps giving me the message we can'tpaste because copy area and paste 
> area aren't the same size. Is there a way totranspose all the data at one 
> time instead of piece by piece? One dataset has agreat amount of rows and 
> columns.
>
> I tried this R function to transpose the datamatrix:
>
> data <- read.table("your_file_ location", sep ="\t", comment.char = "", 
> stringAsFactors = F, header = T)
>
>
> 
> transpose_data <- t(data)
>
> But I received tis error:
>
> unused argument (stringAsFactors = F)
>

You misspelled that argument's name. And do learn to use FALSE and TRUE.

> 
> Is there another way (I prefer a way with Excel)?

This is not a help list for Excel.


--

David Winsemius
Alameda, CA, USA



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-- 
Dan Dalthorp, PhDUSGS Forest and Rangeland Ecosystem Science Center
Forest Sciences Lab, Rm 189
3200 SW Jefferson Way 
Corvallis, OR 97331 
ph: 541-750-0953
ddalth...@usgs.gov



   
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Re: [R] transpose rows and columns for large data

[Elham - via R-help]

yes you have right about excel.by R,what should I do for transposing row and 
column? 

On Tuesday, November 29, 2016 9:13 PM, David Winsemius 
<dwinsem...@comcast.net> wrote:
 

 
> On Nov 29, 2016, at 9:22 AM, Elham - via R-help <r-help@r-project.org> wrote:
> 
> Hi,
> 
> I am trying to transpose large datasets inexcel (44 columns and 57774 rows) 
> but it keeps giving me the message we can'tpaste because copy area and paste 
> area aren't the same size. Is there a way totranspose all the data at one 
> time instead of piece by piece? One dataset has agreat amount of rows and 
> columns. 
> 
> I tried this R function to transpose the datamatrix:
> 
> data <- read.table("your_file_location", sep ="\t", comment.char = "", 
> stringAsFactors = F, header = T)
> 
> 
>  
> transpose_data <- t(data)
> 
> But I received tis error:
> 
> unused argument (stringAsFactors = F)
> 

You misspelled that argument's name. And do learn to use FALSE and TRUE.

>  
> Is there another way (I prefer a way with Excel)?

This is not a help list for Excel.


-- 

David Winsemius
Alameda, CA, USA


   
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[R] transpose rows and columns for large data

[Elham - via R-help]

Hi,

I am trying to transpose large datasets inexcel (44 columns and 57774 rows) but 
it keeps giving me the message we can'tpaste because copy area and paste area 
aren't the same size. Is there a way totranspose all the data at one time 
instead of piece by piece? One dataset has agreat amount of rows and columns. 

I tried this R function to transpose the datamatrix:

data <- read.table("your_file_location", sep ="\t", comment.char = "", 
stringAsFactors = F, header = T)


 
transpose_data <- t(data)

But I received tis error:

unused argument (stringAsFactors = F)


 

 
Is there another way (I prefer a way with Excel)?


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and provide commented, minimal, self-contained, reproducible code.

[R] Duplicate row.names of lncRNA

[Elham - via R-help]

I want to do meta analysis for lncRNA,but there is this error : Duplicate 
row.names are not allowed. 
so 35 genes that are duplicate were detected,for example:
PGM5-AS1-001 ENST0417887.1      
PGM5-AS1-001 ENST0613309.4     
when I search them in ensembl by its Transcript ID, one of them is antisense 
and another is lincRNA, with different bp. why?
for meta analysis,I should aggregate them as mean.is it true in this situation?
is it possible to change name of them by add 1,2.. for example: PGM5-AS1-001.1 
and PGM5-AS1-001.2 ?
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and provide commented, minimal, self-contained, reproducible code.

[R] Duplicate row.names of lncRNA

[Elham - via R-help]

I want to do meta analysis for lncRNA,but there is this error : Duplicate 
row.names are not allowedso some genes that are duplicate were detected,for 
example:PGM5-AS1-001 ENST0417887.1PGM5-AS1-001 ENST0613309.4when I 
search them in ensembl by its Transcript ID, one of them is antisense and 
another is lincRNA, with different bp. why?for meta analysis,I should aggregate 
them as mean.is it true in this situation?
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[R] convert matrix

[Elham - via R-help]

Dear Madam / Sir,I saw this function for "Convert to matrix as it is that you 
wanted" > test2<-as.matrix(test1)
> colnames(test2)<-NULL
> genelist<-c("Fkh2","Swi5","Sic1")
> rownames(test2)<-genelist
> test2
> #  [,1]  [,2]  [,3]
> #Fkh2 0.141 0.242 0.342
> #Swi5 0.224 0.342 0.334
> #Sic1 0.652 0.682 0.182


what is function for large data?my data and genelist are 28031 rows,how can I 
convert? clear that I can not write 28031 genes like 
genelist<-c("Fkh2","Swi5","Sic1")


Your attention would be really appreciated.Best Regards,Elham Dalalbshi Esfahani

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[R] (no subject)

[Elham - via R-help]

Dear Madam / Sir,I saw this function for "Convert to matrix as it is that you 
wanted" > test2<-as.matrix(test1)
> colnames(test2)<-NULL
> genelist<-c("Fkh2","Swi5","Sic1")
> rownames(test2)<-genelist
> test2
> #  [,1]  [,2]  [,3]
> #Fkh2 0.141 0.242 0.342
> #Swi5 0.224 0.342 0.334
> #Sic1 0.652 0.682 0.182


what is function for large data?my data and genelist are 28031 rows,how can I 
convert? clear that I can not write 28031 genes like 
genelist<-c("Fkh2","Swi5","Sic1")


Your attention would be really appreciated.Best Regards,Elham Dalalbshi Esfahani
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and provide commented, minimal, self-contained, reproducible code.