Questions tagged [r]

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38 views

How would we test for significant changes in expression when many of the normalised counts are clustered together?

I've been handed RNA-seq data with a lot of associated covariates. This data has been put through the DESeq2 package and as a result normalised the data. One of the transcripts of interest still has ...
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1answer
35 views

Plot information stored in dataframe within a tree (ggtree)

Hello to the entire Stackoverflow community! I'm writing to you because I'm currently building a phylogeny with ggtree and I have in parallel a table like this one: df : ...
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0answers
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Get dataframe from an LipidomicsExperiment when using lipidr package

With the library lipidr lipidomics data has been normalized using the function normalize_pqn(), and I need to get the normalized data to perform further statistical ...
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0answers
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How to analyze the correlation of two different tissue gene expression under three conditions?

I have three conditions A, B, and C. For each state, I have gene expression data of two different tissues(liver and pancreas). I am studying the possible network/correlation/ between tissues for each ...
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0answers
24 views

EdgeR for DE analysis of RNAseq [closed]

I am doing a DE analysis of RNAseq using EdgeR but there are different functions that look to me that do similar things. I have 4 samples and 2 replicates per sample. I have seen for comparing 2 ...
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1answer
20 views

Extracting concatenated metadata from a column in R

I've downloaded some ChIP-seq data from www.chip-atlas.org and I want to use this to conduct some enrichment tests with genomic regions from my experiment. The .bed file generated by that website is ...
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1answer
24 views

Extracting p-values using corrr package in R

I'm performing correlation analysis using the corrr package in R, but I'm unable to extract the p values. Does anyone know how to get the p values in corrr package in R?
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0answers
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co-expression analysis for two different tissues of same sample

I have gene expression datasets A and B that contain as many rows as genes and as many columns as samples. The rows in A and B represent a common set of genes measured in different tissues of the same ...
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0answers
35 views

Meta-analysis in R [closed]

I am completely new to meta-analysis and am a bit lost on how to proceed. I have two biomarker datasets; each one is using a different microarray platform. I have the protein names, the concentration ...
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1answer
41 views

DESEQ2:Error in rownames, what is the problem?

I am using DESEQ2 for RNAseq analysis but i do not understand why I get this error. ...
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4answers
104 views

I have really skewed RNA-seq data, what's the best way to normalise it? Preferably in R!

My data frame compares the RNA-seq reads from many genes in different tissues. The reads look as follows. I tried using log to make it better but still looks pretty skewed. Are there any better ...
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1answer
31 views

How to download sequence alignments against UniProtKB sequence database for a particular Pfam Id using R?

I am trying to download sequence alignments for families against the UniProtKB sequence database as shown in the example below using R code. Can someone kindly suggest me how to? ...
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0answers
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How to use EPIC DNAm files (.idat) to infer copy number alteration

I have access to EPIC DNA methylation profiles from approximately 40 samples. I want to use these .idat files in order to predict copy number alterations within specific promoter regions of interest. ...
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1answer
29 views

Table error when combining counts columns

I have these files that I want to make table of (https://github.com/learnseq/RNAseqfiles01.git), the table that I want (since all the files have the same ID column),, I want merge the ID column with ...
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1answer
41 views

Splitting data table up based on separate file of gene names

I am very new so bare with me. I have a file called data (.csv that I turned into a data table) with 2 columns (geneid, normalized counts) and about 9000 rows. I have a second file called Xgenes of ...
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1answer
15 views

Error in cor(exprs(gse), use = “c”) : no complete element pairs

I'm trying to plot a heat map for a "GSE133399", I retrieved the GSE using GEOquery package and then assigned to an object and then tried to plot a heatmap, but I was not successful, I used ...
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2answers
56 views

Why is Mann-Whitney U-Test over an ExpressionSet yielding different results than original paper

I am trying to replicate the results of this paper roughly guided by this pipeline. Basically, we are trying to detect a differential expression between mesenchymal and epithelial cells under ...
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0answers
40 views

tissue cross talk using gene expression data

I am studying about tissue cross-talk using gene expression data. My first goal is to identify the genes responsible for communication signaling(cross talk). Let say the tissues are fat and muscle. ...
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1answer
55 views

error in random forest analysis

I am now struggling to do random forest analysis, I will be thankful if you could help with code for random forest analysis. I got samples from the root, soil, and leaf from two regions (bau & mau)...
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1answer
42 views

Too slow issue of BioMart

I am using library(biomaRt) in R to annotate SNP rsid. It takes too much time for only 1000 SNPs....... I would like to know how I can run this code faster. ...
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1answer
36 views

gene-gene correlation from two different Tissues

I am stuck on how to do correlation for two independent data sets with common row and column names. A and B are datasets that contain as many rows as genes and as many columns as samples. The rows in ...
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1answer
42 views

alpha diversity wilcox.test

I am trying to do Wilcox test to detect the significant difference in alpha diversity but it is showing an error? physeqN2 is a phyloseq object and Season is a metadata column. ...
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1answer
29 views

Add segregating sites to branches of a tree

I'm trying to figure out how I would plot a tree with number of segregating sites on display on the branches I'm using acctran from phangorn to plot a parsimony tree (using phydat object from fasta ...
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1answer
91 views

Find intersection among multiple columns and find the intersected elements [closed]

file input file ...
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0answers
45 views

Help importing a biom file into R

How can I import a biom file? When I run the following code: ...
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1answer
49 views

Standard Way to Preprocess Gene Expression?

I am trying to collect gene expression data for the point of fitting gene regulatory networks. My background is primarily in computer science and so I am finding the biological literature a bit ...
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2answers
37 views

How to refine this distribution comparison script

My data look like this They are compound similarity estimations(the whole file is around 10GB). What I am trying to achieve is to compare the similarity distributions of each compound using the ...
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1answer
101 views

DESeq2 - Error in lfcShrink: 'coef' should specify same coefficient as in results 'res'

I have created a DESeq object (dds) and now I want to access the results and apply the lfc shrinkage on them. ...
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2answers
193 views

FPKM, FPKM-UQ, TPM or counts: How do I know which kind of unit should I use?

I'm trying to download data from the TCGA for gene expression analyses in R, but I'm in doubt if I should use FPKM, FPKM-UQ or counts? When the dataset is in counts, I suppose it's raw data, isn't it? ...
2
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1answer
44 views

Microarray Meta-Analysis and Cross-Platform

I have a microarray dataset with Agilent platform, all of the samples are cancerous, I need normal or control samples to compare with cancerous samples, can I combine control samples from another ...
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1answer
60 views

Error When Using biocLite as an installer in rpy2 python library

I am running into an error when I tried to run the following lines of code, the error at line 3: ...
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0answers
16 views

I do not understand the output of ssGSEA using GSVA package in R

I am using the GSVA package in R to do single sample gene set enrichment analysis (ssgsea) using method = ssgsea. This works, ...
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0answers
19 views

Retrieve ATC codes for New Clinical Trials

I have a STATA list of 4000 medicinals used in clinical trials and need to associate an ATC to them. I have scraped wikipedia and BBPharma website and found out some ATCs (missing and None included). ...
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1answer
97 views

Python equivalent to R GRanges and IRanges

Problem: I am trying to convert some codes written in R to Python and part of that conversion process is find classes equivalent to the GRanges and IRanges from the GenomicRanges R package in Python. ...
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0answers
29 views

workaround for error: Bad CPU type in executable c

I use clustal() from library ape every now and then, but now it doesnt work... code: sylvia.clus = clustal(sylvia.seq) Error: ...
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0answers
25 views

About getting rs id from chromosome and position

Hi I have a dataset with chromosome and position. VARIANT_ID chromosome position 17_26797415_147499 17 26797415 17_26797556_147500 17 26797556 How can I ...
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1answer
51 views

Making a union data from different list of genes

I have two groups of patients I have a list of driver genes Clearly each group have mutation in a subset of these gene some of which are common between two groups and some of which are unique to one ...
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1answer
48 views

About the log2 fold change

Hi I have a basic question. It seems that we have two calculations of log fold change. Actual log2(FC) = log2(mean(Group1)/mean(Group2)) Limma's "Log(FC)" = mean(log2(Group1)) - mean(log2(...
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1answer
58 views

TCGA: gene IDs not appearing and other concerns

I want to download RNA-seq datasets of 4 or 5 different types of cancer from the TCGA to investigate what is happening with my gene of interest. The problem is that I'm a physician and I don't know ...
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1answer
57 views

Parsing the json file from gene ontology result into dataframe

How do I parse the json file from ontology output. My file json file jdata <- read_json("analysis.json", simplifyVector = TRUE) I want to convert it ...
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0answers
62 views

Adding legend to Botton and top annotation in complexheatmap

I have a heat map but top and bottom annotation don't have legend ...
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1answer
25 views

Unable to use phangorn::phyDat

I am following an example from ‘Analysis of Phylogenetics Second Edition and Evolution with R’ from Emmanuel Paradis. He is doing: I am doing pretty much the same: ...
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0answers
15 views

Questions about EBSeq (in R)

I have made a UMAP of malignant cells and the result is split into 3 clusters, as seen below. For the sake of example, let's say I want to find the differentially expressed genes in the uppermost ...
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1answer
73 views

Interpreting this plot from GSEA

I have RNA-seq for two groups of patients: Responders to chemotherapy (n=9) versus ...
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1answer
23 views

Error running GenomicVis vcf.venn(vcf.files, 'GRCh38', sample.names)

I am trying to draw venn diagrams with a GenomicVis package (R). library(GenomicVis) It is loaded with a warining: ...
1
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1answer
144 views

Seurat FindMarkers() output interpretation

I am using FindMarkers() between 2 groups of cells, my results are listed but i'm having hard time in choosing the right markers. Do I choose according to both the p-values or just one of them? If one ...
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0answers
23 views

About the Bray-Curtis distance

If we want to calculate Bray-Curtis distance, is it better to use normalize counts using DESseq2 and calculate the proportion (normalized counts by total library size) or is it better to use raw ...
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1answer
48 views

Differentially expressed genes analysis in Seurat

For the differentially expressed genes analysis, is it possible to check for DEGs based on the levels already identified in the object? For example, my dataset contains cells from 11 subjects, which ...
1
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0answers
30 views

How to implement SEG (Wootton and Federhen ,1993) algorithm?

I want to implement SEG in my MATLAB environment and I'm relying on Wootton and Federhen (1993) Reading the article I cannot succeed to understand what kind of process I have to implement in order to ...
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1answer
91 views

Changing active.ident in Seurat

Im trying to change the active.ident to another column in metadata but this error keeps popping up! I recently upgraded to R version 4.0.2 from 3.6.1 The older version was working but the new one isn'...

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