Is it feasible to combine TCGA and GEO data by using ComBat?
Hi, I want to combine these two data sets from different experiments.
When I search for this, many experts didn't recommend to use Combat.
What is the best way you recommend to merge these two sets?
Or, if you consider it as a terrible idea, what's the reason?
Thank you.
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
How to identify regions of similarity/identity that are exclusive for a group within a bigger aling…
written by andre.arrudalima •
-
The difference between merge and integration with Seurat objects
written by re_raz •
-
What is the best annotation tool?
written by Sonia •
-
Refrence datasets for imputation
written by mel22
-
WGCNA, analysis on two data sets
written by halehashki •
-
Merge data set in Plink based on the number of SNPs of the largest
written by @anita •
-
Combining two VCFs each with own set of mutations
written by vctrm67 •
-
Combining two bed bim fam files - genotyped with different panels
written by khn
-
Best way to compare two different pipelines
written by Mozart
-
What is the best test to compare the expression of two different sets of genes in the same transcri…
written by Pas •
There can be no answer to your question considering how you have not explained the data-types that you intend to merge /combine. Which GEO data? - bulk RNA-seq?; cDNA microarray?; scRNA-seq? Which TCGA data? - HT-Seq raw counts?; FPKM expression levels?
TCGA data is RSEM normalized count data downloaded from GDAC and GEO data is expression profiling by array data.
Can I ask what is the benefit of combining the studies rather than looking at them individually? I would urge caution over combining unrelated (institution/author/study) data sets as you would be introducing alot of variables.
I also agreed there is no benefit of combining different sets. I decided not to try it. Thank you for your help and comment:)