Questions tagged [meta-analysis]

The tag has no usage guidance.

Filter by
Sorted by
Tagged with
3 votes
0 answers
48 views

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 ...
user avatar
  • 125
2 votes
0 answers
71 views

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 ...
user avatar
  • 125
0 votes
1 answer
139 views

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 ...
user avatar
0 votes
0 answers
41 views

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 ...
user avatar
0 votes
1 answer
65 views

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 ...
user avatar
  • 159
0 votes
0 answers
30 views

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 ...
user avatar
  • 83
1 vote
0 answers
54 views

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 ...
user avatar