[R] collided row names in heatmap.2

Hi, I am trying to draw a heatmap for my 45 topvar gene by the use of heatmap.2, and when I set a srtRow=45 in my code(below): heatmap.2( assay(rld)[ topVarGenes, ], srtRow=45, scale="row",trace="none", dendrogram="column",col = colorRampPalette( rev(brewer.pal(9, "RdBu")) )(255)) row names

Re: [R] Importing data using Foreign

lem that x[NA] would differ from x[as.integer(NA)] because NA is of > mode "logical", lowest in the coercion hierarchy. > > -pd > > > On 26 Aug 2020, at 17:06 , Elham Daadmehr wrote: > > > > Thanks guys. but I'm a bit confused. the input is the first column >

Re: [R] Importing data using Foreign

0 > z1=z[z[,8]=="11"|z[,8]=="12"|z[,8]=="14",] > sum(is.na(z1[,1])) [1] 399 my file is not compressed. Thank you in advance, Elham On Wed, Aug 26, 2020 at 3:31 PM Eric Berger wrote: > Hi Elham, > You are not giving us much to go on here. > Sh

Re: [R] Importing data using Foreign

> >> Offhand, I suspect that the NAs are in the 8th column. >> >> > On 26 Aug 2020, at 10:57 , Elham Daadmehr wrote: >> > >> > Hi all, >> > >> > I have a simple problem. I get stuck in using the imported spss data >> (.sav) >>

[R] Importing data using Foreign

quot;12"|z[,8]=="14",]), lots of NA appears (even in the first column). The (.sav) file is the output of Compustat (WRDS). It is terrible, I can't find the mistake. Thank you in advance for your help, Elham [[alternative HTML version deleted]] _

[R] Fw: modified mankendal

Hello DearI used modifiedmk package for trend analyses.this is my script  require(modifiedmk)X1<-read.table("c:/elham/first article/r/Spring_NDVI-1.txt",skip=2,header=FALSE)d=dim(X1) outMK<-matrix(-999,nrow=4,ncol=d[2])for (c in 1:d[2]){MK<-tfpwmk(X1[,c])outMK[1,c]<-getEl

[R] How to prepare a input data for Cytoscape

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

Re: [R] filter correlation data

uld 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

[R] filter correlation data

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

Re: [R] caculate correlation

ary 31, 2017 3:07 AM, Jim Lemon <drjimle...@gmail.com> wrote: Hi Elham, What I meant is to simply copy these two expressions into the R command line: coding.rpkm[grep("23.C",coding.rpkm$name),-1] ncoding.rpkm[grep("23.C",ncoding.rpkm$name),-1] and see what co

Re: [R] caculate correlation

ns 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, Th

Re: [R] caculate correlation

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

[R] caculate correlation

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

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

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).

[R] Access GSE Data Tables from GEO by GEOquery

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                                               

[R] GEOquery

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]])[,

Re: [R] help for

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: &g

Re: [R] help for

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

[R] help for

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

Re: [R] calculate correlations

onding 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 ca

[R] calculate correlations

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

[R] memory allocation problem

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

[R] (no subject)

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

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

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,

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

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: > >

[R] transpose rows and columns for large data

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

[R] Duplicate row.names of lncRNA

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

[R] Duplicate row.names of lncRNA

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

[R] store result of meta analysis by Rstudio

hi everyone, how can I store result of meta analysis by Rstudio,I can not save the result of metaseq and metaDE package,I want to use sink to store the output in a file. in metaseq package there are several objects to store:(I copy example of this package) > head(F$Upper) 1/2-SBSRNA4 A1BG

[R] convert matrix

[,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"

[R] (no subject)

[,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"

Re: [R] Convert matrix

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 > [[alternative HTML version deleted]] ___

[R] Fw: R problem

HelloI want to calculate sen slope with out using package. I wrote one but,  it is wrong. I attache my data and my script. would you please check it.Many thanksSincerely yoursElham 1.46 1.22 1.19 1 1.11 1.16 0.78 0.84 0.79 0.85 0.54 0.49 0.61 0.66

[R] Fw: R problem

HelloI am university student.I should do a R home work. That is writing sen slope code in R and calculate it with out using package. I wrote one but,  it is wrong. I attache my data and my script. would you please check it.Many thanksSincerely yoursElham 1.46 1.22 1.19 1 1.11 1.16

Re: [R] About "SpatioTemporal" Package

ards, On Thursday, July 14, 2016 3:10 AM, Jim Lemon <drjimle...@gmail.com> wrote: Hi Elham, It looks to me as though you have created the numeric variable "ID" and then passed it to a function that expects it to be a character variable. Try changing the line: ID<

[R] About "SpatioTemporal" Package

  Dear all,  I want to build the data with the structure of STdata (using the function "createSTdata()"), I did as the following: datst=cbind(xy) yy=cbind(y,xx) ID=60101:60128 date=as.numeric(1:13) y1=as.data.frame(t(cbind(yy))) datst1=as.data.frame(cbind(ID,datst))

[R] From deldir

Dear all, Please guide me in following situation. I use these function from deldir package.   x - runif(20)   y - runif(20)   z - deldir(x,y,rw=c(0,1,0,1))   w - tile.list(z)   plot(w)   ccc - heat.colors(2)   plot(w,fillcol=ccc,close=TRUE) Is each cell red with

[R] (no subject)

Hello, I want to fit linear mixed model for non-normal observation. Which package is appropriate? Thanks [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read

[R] Wrong output in R.14

to receiving your reply. Thank you Elham K.Moez [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html