More posts like this
-
Differential gene expression analysis between species using methods involving read alignment to tra…
written by arsala521 6Hi, My question is about RNA-seq data analysis, particularly differential gene expression analysis between different species. I have RNA-seq reads for a tissue type from …
-
fisher's method for p-value combination in meta-analysis
written by Nelo 2My aim is to conduct a meta-analysis of RNA seq data from different plant species that belong to the same family. I did individual analysis …
-
p-adjusted threshold in pathfindR
written by mrashad 9Dear all, I make a differential expression analysis using t test by multtest package in R under conditions of p-value < 0.05. So the output …
-
Differential gene expression
written by innyus 4Hi all, I am working with differential gene expression on an affy dataset (2 different cancers). I’ve done the analysis using the limma package with …
-
Correlation between gene expression and methylation
written by tujuchuanli 14I have a list of genes and want to test whether the expression level of genes in this list could correlate with DNA methylation level. …
-
Adjusted P-value in GO analysis
written by DNA 0Hi! I am doing GO analysis using software such as EnrichR, and all results come out with good P values but the adjusted P values …
-
50000 significant p values
written by chowdhury 0I have ADNI microarray dataset (https://ida.loni.usc.edu/pages/access/geneticData.jsp#207). The paper says it is normalized data. I have used R -limma package to do the expression analysis among …
-
Low number of differentially expressed genes
written by Biogeek 48Dear all, Pipeline is as follows: Trinity (`min_kmer_cov 3`, `min_glue 3`), CD-HIT-EST followed by CAP3 (for redundancy removal). RSEM for calculating expression values, followed by …
-
box plot problem
written by chowdhury 0Hi, I am trying to do a boxplot in R with normalized TCGA data. I am not getting the box diagram, instead I am getting …
-
How To Interpret Res File Format To Calculate Expression Data
written by monukmr98 8<p>Hi all I am struggling with the RES file format of affymatrix U133+2 platform and its interpretation of P/M/A calls inferences. My specific queries are …