Questions tagged [gene-expression]

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23 questions with no upvoted or accepted answers
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Gene not found in Affymetrix expression profiles

I am studying the ABA network in A. thaliana, consisting of HB7, ABI1 and AREB2. The AGI code I was given are, respectively: AT2G46680, AT4G26080 and AT1G45249. I downloaded the following file in ...
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56 views

Correcting for noise in RT-qPCR gene expression data

I have a training set of RT-qPCR gene expression data (not run in triplicate) for a batch of samples with two phenotypes $A$ and $B$ on which I've trained a "logistic regression classifier". ...
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97 views

How can I collapse probes to single value per gene using GEOquery?

I have extracted microarray gene expression data from GEO using the GEOquery package in R. There are multiple probes per gene. Is there a way to select the best ...
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53 views

How can `limma` be used to determine genes predictive of a given phenotype?

Using limma within Bioconductor here, which is a linear model package for microarray data and lmFit on gene expression data, I ...
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16 views

NMF - Subscript out of bounds

I've calculated the cophenetic coefficients for the NMF of gene expression data, but is giving error when performing the clustering information step as given below: ...
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12 views

How to decide whether to assume 2 Gene Losses or 1 to find minimum cost trees for Gene Duplication/Expression events?

This paper introduces an approach to estimate a convergence from discord between phylogenetic species trees and gene trees, using Gene Duplication and Expression events. A Gene Duplication (GD) event ...
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10 views

How can I associate centrality score of genes(vertices) in a GRN with the probabilistic model in terms of cause and effect?

I'm learning to build Bayesian Network Based Modeling of Gene Regulatory Network of Cancerous Cellular Cells. So far, I have learned to form a Bayesian Network based on nature of genes(i.e Functional ...
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18 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 ...
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20 views

What is the best approach to classify a patient cohort by the expression (low, int, high) of a single gene of interest?

I am working with a dataset of nearly 100 patients. I performed Salmon quantification with genecodeV34 and imported the results with tximeta. I normalised the TPM salmon output with TPM (using edgeR, ...
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245 views

How to convert Illumina IDs to Gene Names?

I am new to the area of bioinformatics, so apologies if this is too obvious of a query. I need to analyze the RNA Seq data from GSE98455. The dataset is of the following format: ...
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1answer
29 views

mapping snp variants to gene expression data

I have a list of SNPs associated with a trait and I'd like to create a list of up- and down-regulated genes associated with these SNPs (using eQTL data I guess). What's the fastest way I could go ...
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23 views

Different results in Differential Expression analysis of Microarray Data

I'm new to R, so be patient with me. I am performing differential gene expression analysis to microarray data for type 2 diabetes donors and nondiabetic donors. when I run the code I get some ...
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18 views

Differential miRNA expression using RPM

I have microRNA (miRNA) expression data in RPM. I would like to do differential gene expression between two groups. How can I do this? I have considered edgeR and DESeq2 in R, but it looks like they ...
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22 views

How to merge several microarray-based gene expression datasets while not excluding genes that are not present in all datasets?

In integrative gene expression analysis when two expression matrices from different datasets are merged together, they are usually merged by common genes in both expression matrices while all other ...
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61 views

Troubles implementing LIMMA for paired samples (before/after treatment) comparaisons

i try to implement LIMMA for paired samples in order to compare gene expression before/after treatment. But...i'm not confident in my results since every single gene expression seems to be ...
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27 views

Opening gctx files

I installed cmapPy but I don't know how to use it to read gctx files. I read the documentation. If anyone knows how to do it with cmapPy or any faster method your help would be greatly appreciated. I ...
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35 views

MEME's motifs have an E-vaue too high

I'm currently learning how to use MEME-Suite (web tool) to find a specific known transcriptor binding site in the promoter region of 5 putative bacterial genes of interest, but the results obtained ...
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93 views

Unable to gunzip fastq files from ENA

I am trying to process fastq files in order to build gene co-expression networks (by following this tutorial). When I download any fastq file from ENA, and try to process it with the command: ...
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29 views

How do I generate a list of post-synaptic gene markers that will guide me in my search for these markers in intestinal stem cells?

I would like to generate a list of gene markers that represent post-synaptic related genes. I will then use this list to search through single cell sequencing data, in order to assess whether certain ...
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185 views

Create a Heatmap that uses modules of genes rather than individual genes in Seurat

Is it possible to create a Heatmap in Seurat that takes in and displays modules of genes as its features rather than individual genes? So if I have a module of genes associated with a trait or ...
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2k views

Create heat map that groups genes by expression within cluster in Seurat

I have a set of cells that I am performing Drop-seq on to look at cell expression. Among my heat maps for gene expression I want to be able to graph them similar to the graph below: Where the cells ...
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64 views

Any way to filter out highly correlated genes with limma linear model?

I have Affymetrix gene level expression matrix (genes in the rows and sample ID on the columns), and I have annotation data of microarray experiment observation where sample ID in the rows and ...
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133 views

Question about enrichment score (ES) and NES from GSEA

I have two results from separated two GSEA runs, and i want to know which sample has the most enrichment about specific pathway (gene set). Can I use ES (or NES) from two different GSEA analysis ...