Questions tagged [correlation]

Statistical term describing the association of two variables in accordance with a significance measure

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Why are my Chi-squared test results different from those in a published table?

I recently read the paper “A novel long non-coding RNA linc-ZNF469-3 promotes lung metastasis through miR-574-5p-ZEB1 axis in triple negative breast cancer”. In this I see Table1 showing correlation ...
stack_learner's user avatar
4 votes
1 answer
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How to calculate module-trait relationship when trait data is in binary format?

I have a dataset of 50 breast cancer samples. These samples are classified into four subtypes Lum A, Lum B, Her2 and Basal. I have been working with lncRNAs and protein-coding genes. To identify the ...
user9114's user avatar
3 votes
2 answers
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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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Different results of spearman correlation between TPM and FPKM

TPM and FPKM of RNA-Seq data form GDC TCGA calculated based STAR were retrieved, respectively. The correlation between a specific gene, e.g. HIF1A, and other genes were calculated based on TPM and ...
Yang Shi's user avatar
2 votes
1 answer
134 views

RNA-Seq data transformation prior to sample correlation analysis

If I’m starting with Deseq2 normalized counts what are some preprocessing steps that I should apply to these data before estimating sample correlation using the cor function in R? For example, would ...
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Extracting genes from corrplot and adding labels based on high and low corelation

I am doing a gene-gene pairwise correlation, I get a plot and I do see positive and negative correlation My code: ...
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2 votes
1 answer
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How to get separate histograms plots on the basis of the column value?How to detect which plot has most deviation?

I have a data frame (df) which has correlations calculated for different genes with respect to different ID combinations. I want to get separate histogram plot based on the gene name (separate plot ...
Riya's user avatar
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2 votes
1 answer
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correlation between imputed genotype and true genotype

There is a graph in the link https://odelaneau.github.io/GLIMPSE/rsquare_eur.html. This graph shows the imputation accuracy of certain MAF bins. Now I understand that $r^2$ is the correlation between ...
Shafayet Rahat's user avatar
2 votes
1 answer
47 views

How to prove correlation between gene expression and functions using omics data in bioinformatics?

I am new to bioinformatics, coming from a background in mathematical biology. I am currently participating in a project where the Principal Investigator (PI), who is a biologist, has tasked me with ...
LOVEMATH's user avatar
2 votes
1 answer
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Generate a single column from two different columns in the same format

I have multiple data frames in R in the following format: Dataframe1: ...
DEEP's user avatar
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2 votes
1 answer
189 views

Identifying mutually **exclusive** gene sets

I am interested in identifying gene pairs (or better: sets of genes) whose expression is mutually exclusive. Ideally, both genes (or gene sets) would be widely expressed but I am also interested in ...
Paul Brodersen's user avatar
2 votes
1 answer
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Metagenomic shotgun data with internal control

For 24 human stool samples I have metagenomic shotgun reads from an Illumina platform. The reads were filtered and mapped against a bacterial species library and specific maps to species were kept and ...
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2 votes
1 answer
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Which values from Seurat::FetchData function are to be used for correlation analysis between genes?

I want to perform a correlation test between genes in on my single cell RNA seq data set. I perfomed the differential expression analysis using the Seurat version 2 package, after performing stages of ...
Charles's user avatar
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1 vote
1 answer
608 views

Spearman correlation between two genes

I have FPKM data for three genes like below: ...
stack_learner's user avatar
1 vote
1 answer
2k views

How to specifically select cluster on Featurescatter on Seurat?

Nowadays, I am trying to calculate Pearson correlation values between two genes of my interest from single-cell RNA-data (features.tsv, barcodes.tsv, and matrix.mtx files) which are obtained from the ...
raiora's user avatar
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1 vote
1 answer
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correlation coefficient versus DEGs analysis: what's the best approach for low expressed genes?

I have 6 folders. Each one contains 7 datasets of a specific type of cancer (RNA-Seq) and 7 datasets of normal tissue (healthy control for that type of cancer). A total of 84 datasets. I want to ...
FPS's user avatar
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1 vote
2 answers
68 views

How to exclude the repetition of gene-gene correlation calculation in python?

I am trying to make a paired matrix of gene-gene correlation. Considering that I have a huge matrix (13000 genes and 900 samples) and for some reasons I don't want to decrease the number of my genes, ...
Elyas Mohammadi's user avatar
1 vote
2 answers
212 views

Multiple correlation with R

I have a data frame presenting different variables in column and for different species name in rows as follow. In the column a have only one independent variables(Proteome size) and all the others are ...
Dieunel Derilus's user avatar
1 vote
0 answers
102 views

Correlate ssGSEA score with Seurat's scaled expression data

I want to check the correlation between the expression of a given "test_gene"* in each cluster within a scRNA-seq database with the expression of a signature (i.e., gene sets whose ...
samge's user avatar
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1 vote
0 answers
27 views

How to investigate the correlation between transcript and protein abundance?

Our study shows that gene A knockout will down-regulate cell cycle-related genes in some cell lines. My aim is to understand whether cell cycle-related genes are down regulated on the transcriptional ...
Wang Ming's user avatar
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1 vote
0 answers
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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 ...
data's user avatar
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1 vote
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Regarding RNA seq data analysis and building coexpression network

I have some questions regarding RNA seq analysis if you can suggest anything it will help me a lot. I am currently normalizing RNA seq data for comparing genes expression within and between samples. ...
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Algorithmic Information Measurement of Human Genome Databases?

What is the highest data compression ratio achieved on a population of genomes measured to include the compressing algorithm itself? The size of the compressed database approximates its algorithmic ...
James Bowery's user avatar
0 votes
1 answer
699 views

Power law distribution alpha values

I did a Pearson co-expression analysis for generating networks for my tissue-specific (chondrocytes) RNA-seq data. I used R package poweRlaw to check for the power-law distribution. We got the ...
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1 answer
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Error in formation of correlation matrix-(corrupt matrix -- dims not not match length)

I am working on a script to create a correlation matrix and mutual_rank matrix from RNAseq gene counts for 57992 genes in 7027 samples. I have already tested this script for a smaller file (for 10,000 ...
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1 answer
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I am trying to find correlation between two ChIP-seq datasets but the Pearson and Spearman test results do not correspond with the peak overlap

I am trying to compare two ChIP-seq datasets for histone modifications, however, the Spearman and Pearson correlations between two particular datasets does not correspond to their peak overlap (peak ...
Rafay Ali Khan's user avatar
0 votes
1 answer
102 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 ...
data's user avatar
  • 123
0 votes
1 answer
2k views

How to remove zero value of gene on FeatureScatter plot using Seurat?

Nowadays, I am trying to calculate Pearson correlation values between two genes of my interest from single-cell RNA-data (features.tsv, barcodes.tsv, and matrix.mtx files) which are obtained from the ...
raiora's user avatar
  • 77
0 votes
1 answer
112 views

How to analyze co-occurrence of multiple SNPs?

I am interested in 20 different SNPs that all are either As or Gs, and they all occur on the same chromosome. How can I assess the co-occurrence of these SNPs? In other words, I want to know, if SNP1 ...
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1 answer
56 views

correlation between transposon and gene

I have two matrix identical in N° of rows and columns. In the first matrix rows indicate transposable elements and columns indicate samples. the matrix show the degree of expression of each element ...
jonny's user avatar
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1 answer
254 views

Correlate DEGs from DESeq2, EdgeR and Limma results

I have a lists of DEGs identified by DESeq2, EdgeR and Limma. I would like to correlate the the gene rankings in the lists to decide on a package to use in downstream analysis. I am havig a few ...
Lyd's user avatar
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1 answer
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Help with analyzing SNP data for three patient groups

I am currently working on a project where I have genetic data for patients classified into three different groups. Specifically, I have information on 26 SNPs for each patient. I have recorded each ...
Ismael Prieto's user avatar
0 votes
0 answers
53 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. ...
data's user avatar
  • 123
0 votes
1 answer
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P-value correction when evaluating correlation between gene and miRNA expression

First of all I apologize without the question is very basic, I am taking my first steps in bioinformatics. Data information We are evaluating the correlation (using the Pearson, Kendall or Spearman ...
Genarito's user avatar
  • 101
-1 votes
3 answers
257 views

Is it possible to do this in R?

I have a big clinical data file with 96 columns like age, gender, BMI, etc I want to see which of these clinical characteristics respond to chemotherapy. Response to chemotherapy divides patients to ...
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