Questions tagged [meta-analysis]
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Analysing the Effect of a Drug on the Morphological Changes of a Cell Type
We came across a project in our lab that no one exactly knows how to approach. Since, I know a little bit of Python programming, this project was assigned to me. There is a data from a randomised ...
Heat map of protein expression from normalized abundance
This is a follow up to my question posted here Processing proteomics data In relevance to my research, I've been looking for proteomics data (control vs. diabetic) and I found a dataset in the article ...
Help with performing PCA analysis on data from 3 different datasets of normalized counts data for RNA-seq experiment
So, I have limited knowledge of R but I need to do a PCA analysis of 3 different datasets of gene expression as a result of combined growth or mono-culture growth. The 3 different datasets I performed ...
How to tune and use the MetaVolcanoR package
I conducted a differential expression analysis over several datasets, using LIMMA, each one on its own. For each dataset, I have a data frame of all the genes, with ...
Applying colocalization analysis in Asian populations
I am planning to add colocalization method as a post-GWAS analysis in my study which is solely based on east Asian populations. I have noticed that coloc, enloc and eCaviar are being commonly used for ...
Setting up MaxQuant parameters for processing proteomics data
This is a follow up to my previous question here. In relevance to my research, I've been looking for proteomics data (control vs. diabetic) and I found a dataset in the article "Diabetes causes ...
How to perform a meta-analysis using data consisting of paired-end and single-end reads generated from Illumina and Ion Torrent?
So basically I have RNA-seq reads that were generated from Illumina and Ion Torrent platforms for yeast species. I have seen an article where they compared liver cells of a rat that were sequenced ...
Combining read counts from three separate GEO studies
I want to do differential expression analysis with DESEQ2. I have three read counts files downloaded from GEO (small RNAseq based) where the number of miRNAs and id is nearly the same. These studies ...
How to decide between standardized mean difference (SMD) and log2fold change (log2FC) before doing meta-analysis?
I want to do meta-analysis of alpha diversity between test and control groups across 10 different populations. I want to see what is the summed effect (pool effect) of intervention between the two ...
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 ...