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Questions tagged [gene-expression]

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40 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, ...
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17 views

What should I do when I have “#NAME?” in my Log Fold Change data to calculate Z-score? replace with zero or what?

I am trying to calculate the Z-score for several columns with Log fold change (LFC) data from RNA-seq expression values. But the mean for all columns, except one of them, is -inf and the standard ...
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1answer
37 views

Interpreting a kernel density function plot of gene expression

I need help interpreting a kernal density plot and a histogram of this data. I have provided some context below let me know if you need more information A co-worker that I am collaborating with has a ...
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1answer
109 views

Doing plot with this data

I have normalized expression values of some genes in some patients and the how many days they have survived from their diagnosis with cancer like below EDITED I have taken mean of the expression ...
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66 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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2answers
53 views

Find most similar genes to a set of genes of interest in time series RNA-seq data

I have gene expression data (RNA-seq) for 30 different time points (from 0 to 60 min each 2 min). I have a set of 8 genes that behave similarly (although not identically) and I want to find the top X ...
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379 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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1answer
50 views

Finding drugs based on gene expression data

I've got a list of genes and I want to assess their association with drugs based on gene expression data sets. A comprehensive tutorial would also be helpful. Any help would be appreciated.
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53 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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1answer
25 views

Any way to quantify the variation of genes that expressed in Affymetrix expression data?

am experimenting preprocessed Affymetrix microarrays expression data matrix (Affymetrix probe-sets in rows (32830 probesets), and RNA samples in columns (735 samples)) for my downstream analysis. Here ...
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1answer
38 views

What's the difference between gene expression profiles and images?

What's the difference between gene expression profiles data in genomics and images data in computer vision? What's the characteristic of the profiles? (not just high dimension and low samples) The ...
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72 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 ...
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34 views

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

Using limma and lmFit on gene expression data, I can perform a series of regressions ...
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2answers
79 views

residual Squared Coefficient of Variation (rCV²) vs Distance to Median (DM)

I am working with single cell RNA-seq data. I obtained the squared coefficient of variation (CV²) as a measure of gene expression variability: I want a metric to express gene expression noise that ...
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1answer
231 views

Clustering of gene co-expression network by igraph R package

I have constructed a gene co-expression network from RNA-seq data. The network has more than 10000 nodes and more than 1 million edges. The network file as an edge list format of memory around 1gb ...
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1answer
125 views

How to extract gene expression tables from this GEO dataset?

I've downloaded this GSE43013 dataset using GEOquery in R. My understanding is that it contains expression data from liver, kidney, and brain for multiple species. I would like to produce gene ...
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1answer
55 views

I need some tips and suggestions for further analysis of NGS expression data (log2cpm)

I am a PhD student who inherited some log2cpm data of expression data from bulk kidney tissue from a UUO(unilateral urethral obstruction) experiment that tests a new drug. The sample material consists ...
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2answers
173 views

How to cluster the human genes by pathways/system-biology/metabolic properties?

I would like to make a chord plot from my data. I have a list of genes that according to my experiments are divided into 64 clusters of enrichment pattern. I would combine my 64 clusters with a ...
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1answer
60 views

How can I interpret gene expression data from Bioconductor packages?

I am currently looking at microarray data from a bioconductor microarray dataset. Specifically, I have data (a snippet) which looks like the following: ...
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1answer
145 views

Gene Ranking - signal to noise ratio used in GSEA-P algorithm?

I'm looking at Broad Institute's orignal GSEA-P algorithm R script which I downloaded here: http://software.broadinstitute.org/gsea/downloads.jsp. I'm trying to adapt their GSEA.1.0.R script to ...
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3answers
1k views

How to quantile normalization on RNA seq counts

I have a read count data (RNAseq) and want to perform quantile normalization. Could you please help me how to do it. I tried some scripts in R but it didn't work. I want the result output in matrix ...
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2answers
94 views

Why the t-test for a specific gene shows different value compared to differential analysis?

I have RNA-Seq data for LUNG cancer. 370 tumor and 50 Normal. For differential analysis initially I did some filtering and kept approx. 19k genes for further analysis. I used edgeR. With a FC > or &...
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41 views

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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2answers
605 views

How to deal with duplicate genes having different expression values?

I have RNA-Seq data which is FPKM. In the dataframe df first column is gene_name and the ...
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2answers
2k views

How to convert featureCounts to FPKM?

I have seen many posts regarding counts to RPKM and TPM. I haven't seen any post for counts to FPKM. I have RNA-Seq data which is paired-end reads. Extracted the counts using featureCounts for all ...
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1answer
63 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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37 views

What information can be extracted from this GEO file name?

I could not find any information regarding the conventions of naming files of processed data in GEO, so I don't know what to assume about the data of a file named ...
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2answers
206 views

Find a cutoff value for genes that are expressed in single cell RNA-seq?

I want to find a cutoff value for each gene, above which we can consider a gene expressed. The problem is that not all effectively non-expressed genes will have 0 counts due to sequencing errors for ...
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2answers
57 views

Comparing the gene expression data

I'm trying to compare the gene expression data reported in the studies documented in GEO for a specific gene expressed in a tissue of my interest in Homo sapiens. I compared the values reported in 4 ...
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0answers
52 views

Parsing gene expression value for a list of genes from GEO

I am looking for the gene expression data in GEO GSE15543 with the following keywords, (Pancreatic Beta Cells) AND "Homo sapiens"[porgn:__txid9606] I would like ...
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0answers
32 views

Quality checking benchmarks for clustering

I'm currently working with several RNAseq datasets from the ENCODE database. My approach to assessing the quality of the data, i.e, reproducibility is by automating the assessment of expression ...
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0answers
35 views

Find Dataset of human genes in GEO datasets

I am trying to build model to predict relation between diseases and genes using genes features. I have a list of genes that I am interested in. I need to get gene expression of specified genes from ...
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1answer
249 views

Get Gene Expression Matrix from GEOquery

I am trying to get gene expression matrix for a list of genes I have for my list: Gene ID, Gene Symbol How can I get for each gene corresponding expression as array?? I suppose that I will have ...
3
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2answers
103 views

Convert Cotton Probe ID to Gene Symbol

I am new to bioinformatics, my background is in Electrical Engineering. I am trying to convert Affymetrix Cotton Probe IDs to gene symbols. I have a gene expression dataset and I need the expressions ...
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1answer
37 views

Where to download baseline/average gene expression level of all human coding genes?

I am looking for the most appropriate dataset for downloading baseline gene expression level across all human coding genes during development. I am aware that EMBL Expression Atlas is one of the ...
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0answers
41 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. I also ...
2
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1answer
36 views

Why models of stochastic gene expression predict that intrinsic noise should increase as the amount of transcript decrease

I am reading Elowitz et al. (2002). When talking about intrinsic noise, i.e. noise due to microscopic events that govern which reactions occur and in what order, it is stated that: Models of ...