RSEM expected_count vs normalized_count

I am wondering what is the difference between RSEM expected_count vs normalized_count and which one should be used for DESeq2 or EdgeR.

rna-seq

• 3,468 views • link

updated 5.6 years ago by noorpratap.singh

• written 5.8 years ago by Pappu

1 answer

Have a look at these posts Interpreting TCGA .rsem.genes.results and .rsem.genes.normalized_results files.
Question about how to transform RSEM expected_count of TCGA TARGET GTEX to integers?.
You should use expected_count as the input, provided it has not been transformed.

• 0 views • link

written 5.6 years ago by noorpratap.singh

More posts like this

Pooling replicates for CHIP-seq peak calling
written 5.7 years ago by Pappu

I am wondering what is the difference between pooling 2 replicates and 2 IGG controls for ChIP-seq peak calling compared to running the peak calling …
Adapter and barcode trim off
written 5.8 years ago by Bio_Crap •

Hi all, I just started to learn metagenomics. I am wondering what is the difference between adapter vs. barcode. Where should I look at adapter …
Difference between PERMANOVA and DESeq2 analysis for amplicon sequencing
written 7.2 years ago by Bioinfonext

Hi, I am not able to understand what is the difference between `PERMANOVA` and `DESeq2` analysis for `amplicon microbial analysis`. I do have amplicon sequencing …
Question about how to transform RSEM expected_count of TCGA TARGET GTEX to integers?
written 7.2 years ago by dz2353

Hi, there I downloaded RSEM expected_count data of TCGA TARGET GTEX from UCSC Xena to perform differential expressed analysis. I noticed the unit is log2(x+1), …
basic experimental methods book for bioinformaticians
written 7.4 years ago by Pappu

I am wondering if the is any basic experimental methods book or review for bioinformaticians so that they can understand the presentations given by experimentalists. …
DE and enrichment analysis pipeline
written 7.5 years ago by Pappu

I am wondering if there is any pipeline which runs DESeq2, EdgeR etc DE analysis and GSEA, Pathway etc enrichment and other basic analysis in …
RSEM log 2(norm count +1)
written 8.1 years ago by saumram •

hello! I was wondering how one could interpret RSEM log2(norm_count +1) difference between Control = 1 and Treatment = 8 for a given gene. Is …
Difference between MrBayes and Beast MCC tree
written 10.5 years ago by Pappu

I am wondering what is the difference between the trees if one uses same substitution models like gtr + gamma.
Differential expression analysis for TCGA level 3 RNASeqV2 data?
written 11.8 years ago by cafelumiere12

Hi! I am actually looking at TCGA level3 RNASeqV2 data. My goal is to look at the DEGs (tumor vs. normal) and I'm looking at …
[DESeq2 multiple treatments vs. 1-by-1] Inconsistant p-adj
written 12.0 years ago by madkitty

So we have RNAseq data for 3 treatments (A, B and C) that we compared to control. Each treatment should be compared to control (as …