[R] DrDimont package in R

[[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 com

Re: [R] Count matrix of GSE146049

microarray data. > > HTH, > > Peter > > On Sun, Apr 2, 2023 at 11:09 PM Anas Jamshed > wrote: > > > > I want to get the count matrix of genes from > > https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE146049. Is it > > possible fo

[R] Count matrix of GSE146049

I want to get the count matrix of genes from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE146049. Is it possible for GSE146049? After getting counts, I want to do TMM normalization. [[alternative HTML version deleted]] __ R-help@r-proje

[R] Read excel specific column

I have .xlsx files with gene names in first column.How can read and load in R? [[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

Re: [R] Normalize GEO Data

I mean how can I apply RMA to my datasets? On Mon, Aug 15, 2022 at 9:50 PM Bert Gunter wrote: > I have no idea what you mean. Please do *not* respond to me privately. > > On Mon, Aug 15, 2022 at 9:48 AM Anas Jamshed > wrote: > > > > but how can I apply for RMA? > &g

[R] Normalize GEO Data

I performed GEO2R analysis on a series dataset and I'm looking to find the up-regulated and down-regulated genes. I know that to find up-regulated and down-regulated genes, I should check logFC (Fold-change in log2 scale (generally)).Consider the value of 1 in log2 is 0. There is optimal cutoff but

[R] Connect R with Ensemble Rest API to fetch variations

I have a list of 422 genes in excel file .I want to know if its possible to get snps details of these gene by using Ensemble Rest API or biomart? [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and mor

Re: [R] Need help to print matrix with element and position

where should I place cat(row,col,mat_1[row,col],"\n")? On Thu, Oct 28, 2021 at 1:58 PM Jim Lemon wrote: > Hi Anas, > How about: > > cat(row,col,mat_1[row,col],"\n") > > Jim > > On Thu, Oct 28, 2021 at 7:19 PM Anas Jamshed > wrote: > > >

[R] Need help to print matrix with element and position

I create a matrix of size 3x3 called mat_1 and then I want to iterate over all the values one by one and print the element as well as the position in the matrix: My code is : mat_1= matrix( c('1','2','3','4','5','6','7','8','9'), nrow = 3, ncol = 3,byrow = TRUE) mat_1 # Loop over my_matrix for(ro

Re: [R] Need help in R

(f == 1) { print(paste("Number is prime :", n)) } } On Wed, Oct 27, 2021 at 1:35 AM Rolf Turner wrote: > > On Wed, 27 Oct 2021 01:09:50 +0500 > Anas Jamshed wrote: > > > I need help to these questions > > > > ### Question 1 > > C

[R] Need help in R

I need help to these questions ### Question 1 Create a variable containing a sequence of numbers from 1 to 100: Iterate over the variables and print those numbers which are prime. ### Question 2 Create a matrix of size 3x3 called mat_1: Iterate over all the values one by one and print the ele

[R] Gene Set Enrichment Analysis and plots

I have done this analysis: #You can select Working Directory according to your choice setwd("D:") #Check Working Directory getwd() #Creation of object(folder) exdir exdir <- path.expand("~/GSE162562_RAW") dir.create(exdir, showWarnings = FALSE) URL <- " https://ftp.ncbi.nlm.nih.gov/geo/series/G

Re: [R] Need help to unzip files in Windows

ist.files(exdir, full.names = TRUE) > names(files) <- sub("\\.txt\\.gz$", "", basename(files)) > > > # R can open compressed files without decompressing beforehand > print(utils::read.table(files[[1]], sep = "\t")) > print(utils::read.delim(fil

Re: [R] Need help to unzip files in Windows

gt; utils::download.file(URL, FILE, mode = "wb") > utils::untar(FILE, exdir = dirname(FILE)) > > > worked perfectly for me. It seems to also work still on Ubuntu, but you > can let us know if you find it doesn't. I hope this helps! > > > > On Mon, Aug 23,

Re: [R] Need help to unzip files in Windows

) > utils::untar(FILE, exdir = dirname(FILE)) > > > and it makes a folder "Image-ExifTool-12.30". It seems to work perfectly > fine in Windows 10 x64 build 19042. Can you send the specific file (or > provide a URL to the specific file) that isn't working for you? > &g

[R] Need help to unzip files in Windows

I have the file GSE162562_RAW. First I untar them by untar("GSE162562_RAW.tar") then I am running like: system("gunzip ~/Desktop/GSE162562_RAW/*.gz") This is running fine in Linux but not in windows. What changes I should make to run this command in windows as well [[alternative HTML ve

Re: [R] Differential Gene Expression in R

is available. You will still have to learn a little about > edgeR analysis, so reading the vignette will be very helpful. > > Also, for the comparisons you want to do, statistical help is > recommended. > > Matthew > > On 8/22/21 2:13 PM, Anas

[R] Differential Gene Expression in R

I have downloaded data from: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE162562&fbclid=IwAR0iZQhttG8HzGhFIIMWbFgNszQrVDgiyVChYzQ_ypCx_d-1pn_tm7STjGs and now I want to compare: healthy vs Mild healthy vs Highly exposed seronegative (ishgl) Healthy vs Asymptomatic covid19 patient healthy

[R] differential gene expression

I have this data: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE162562&fbclid=IwAR0iZQhttG8HzGhFIIMWbFgNszQrVDgiyVChYzQ_ypCx_d-1pn_tm7STjGs and I want to compare: healthy vs Mild healthy vs Highly exposed seronegative (ishgl) Healthy vs Asymptomatic covid19 patient healthy vs Highly expose

[R] (no subject)

when I tried to install oligo package by if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("oligo It gives me the following eroor: Warning messages: 1: In file.copy(savedcopy, lib, recursive = TRUE) : problem copying C:\Users\USER\

[R] How to save Results in svg format

#Loading the required libraries library(ape) library(phangorn) library(seqinr) #Importing the required file align_5 <- read.alignment("C:/Users/VAMSI/align 5.fasta", format = "fast") align_119 <- read.alignment("C:/Users/VAMSI/align 119.fasta", format = "fasta") Computing the distance matrix for bo

[R] Save Results in svg format

#Loading the required libraries library(ape) library(phangorn) library(seqinr) #Importing the required file align_5 <- read.alignment("C:/Users/VAMSI/align 5.fasta", format = "fast") align_119 <- read.alignment("C:/Users/VAMSI/align 119.fasta", format = "fasta") Computing the distance matrix for bo

[R] Need help to calculate allele score

Go to page http://zzz.bwh.harvard.edu/plink/profile.shtml and follow the help to generate a basic allele score using your independently associated SNPs. Use R to make the myprofile.rawfile required. I am unable to generate .raw file which will contain allele score I have tried this script: resul

[R] DEG Analysis in R through Bioconductor

Basically I want to redo the methodology of the paper: https://www.nature.com/articles/s41598-018-23492-2 I choose microarray data GSE75693 of 30 patients with stable kidney transplantation and 15 with BKVN to identify differentially expressed genes (DEGs). I performed this in GEO2R and find R scri

[R] RNA Seq Analysis in R

I choose microarray data GSE75693 of 30 patients with stable kidney transplantation and 15 with BKVN to identify differentially expressed genes (DEGs). I performed this in GEO2R and find R script there and Runs R script Successfully on R studio as well. The R script is : # Differential expression