Questions tagged [r]
Please supplement your question with a minimal reproducible example. Use dput() for data and specify all non-base packages with library calls. For statistical questions please use http://stats.stackexchange.com.
607
questions
0
votes
2answers
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 ...
2
votes
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 :
...
0
votes
0answers
15 views
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 ...
0
votes
0answers
15 views
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 ...
0
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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 ...
0
votes
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 ...
2
votes
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?
1
vote
0answers
12 views
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 ...
1
vote
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 ...
-1
votes
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.
...
2
votes
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 ...
1
vote
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?
...
1
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0answers
12 views
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. ...
0
votes
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 ...
1
vote
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 ...
0
votes
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 ...
0
votes
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 ...
0
votes
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.
...
1
vote
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)...
-1
votes
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.
...
0
votes
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 ...
0
votes
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.
...
1
vote
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 ...
-1
votes
1answer
91 views
0
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0answers
45 views
0
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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 ...
2
votes
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 ...
1
vote
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.
...
0
votes
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
votes
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 ...
0
votes
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:
...
0
votes
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, ...
0
votes
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). ...
1
vote
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. ...
0
votes
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:
...
0
votes
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 ...
-3
votes
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 ...
-1
votes
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(...
1
vote
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 ...
0
votes
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 ...
0
votes
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
...
0
votes
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:
...
1
vote
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 ...
0
votes
1answer
73 views
Interpreting this plot from GSEA
I have RNA-seq for two groups of patients: Responders to chemotherapy (n=9) versus ...
0
votes
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
vote
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 ...
0
votes
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 ...
1
vote
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
vote
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 ...
0
votes
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'...
