Questions tagged [correlation]

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

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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: ...
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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 ...
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How should I use FDR p-value correction in case of multiple subject with multiple parameters?

In my experiment I have 45 subject. On each subject we measured two set of paramaters. Set A contains 23 and set B contains 203 unique parameter. I use spearmann correlation test to find connenction ...
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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 ...
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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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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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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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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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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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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 ...
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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 ...
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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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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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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 ...
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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 ...
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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
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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 ...
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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 ...
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1 vote
2 answers
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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, ...
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-2 votes
3 answers
216 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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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 ...
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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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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 ...
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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 ...
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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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Removing genes with less than a correlation cut-off between two matrices

I have two matrices like this: ...
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2 votes
1 answer
1k views

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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1 vote
2 answers
189 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 ...
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4 votes
1 answer
94 views

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 ...
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1 vote
1 answer
471 views

Spearman correlation between two genes

I have FPKM data for three genes like below: ...
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