Collapse technical replicates in DEGS
Hi, I am analyzing RNA-seq samples from 4 different cell lines. The goal is to identify differentially expressed genes (DEGs) between control and treated samples at day 1,3 and day 6. I have 3 replicates for each condition. Given below is the metadata,
| Sample | Cell Line | Day | Treatment | |
|---|---|---|---|---|
| Day1_A_A | A | 1 | Treated | |
| Day1_A_A1 | A | 1 | Treated | |
| Day1_A_A2 | A | 1 | Treated | |
| Day1_A_AC | A | 1 | Control | |
| Day1_A_AC1 | A | 1 | Control | |
| Day1_A_AC2 | A | 1 | Control | |
| Day3_A_A | A | 3 | Treated | |
| Day3_A_A1 | A | 3 | Treated | |
| Day3_A_A2 | A | 3 | Treated | |
| Day3_A_AC | A | 3 | Control | |
| Day3_A_AC1 | A | 3 | Control | |
| Day3_A_AC2 | A | 3 | Control | |
| Day6_A_A | A | 6 | Treated | |
| Day6_A_A1 | A | 6 | Treated | |
| Day6_A_A2 | A | 6 | Treated | |
| Day6_A_AC | A | 6 | Control | |
| Day6_A_AC1 | A | 6 | Control | |
| Day6_A_AC2 | A | 6 | Control | |
| Day1_B_B | B | 1 | Treated | |
| Day1_B_B1 | B | 1 | Treated | |
| Day1_B_B2 | B | 1 | Treated | |
| Day1_B_BC | B | 1 | Control | |
| Day1_B_BC1 | B | 1 | Control | |
| Day1_B_BC2 | B | 1 | Control | |
| Day3_B_B | B | 3 | Treated | |
| Day3_B_B1 | B | 3 | Treated | |
| Day3_B_B2 | B | 3 | Treated | |
| Day3_B_BC | B | 3 | Control | |
| Day3_B_BC1 | B | 3 | Control | |
| Day3_B_BC2 | B | 3 | Control | |
| Day6_B_B | B | 6 | Treated | |
| Day6_B_B1 | B | 6 | Treated | |
| Day6_B_B2 | B | 6 | Treated | |
| Day6_B_BC | B | 6 | Control | |
| Day6_B_BC1 | B | 6 | Control | |
| Day6_B_BC2 | B | 6 | Control | same for cell line C and D. How should I design the experiment for the analysis, and how can I collapse replicates? Thank you. |
• 676 views
•
link
updated
by
Ram
•
written
by
drajangirija •
•
written
by
drajangirija •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
DEseq2 interactions
written by drajangirija •
-
How to solve DESeq2 Error in checkFullRank(modelMatrix) cause by biological replicates information?
written by ace •
-
Bulk RNA sequencing time course pathway analysis progression visualization
written by Fred •
-
Multi factor analysis in DESeq2 and design formula
written by nik.kraemer •
-
Design Matrix with EdgeR or DESeq2
written by reui879 •
-
Proteomics Data Analysis
written by osamashehzad.786 •
-
Ribo-Seq multi time course analysis with DESeq2
written by hibernicah •
-
maintaining a cell lineage population
written by rob.costa1234
-
how to arrange data for pathway analysis ?
written by Learner
-
DESeq2 model design: dose and time effect
written by CuriusScientist
From title
Just so we have clarity
A/A1/A2are the same cell line sample library A from day 1 run on three lanes/flowcells? That would be a technical (sequencing) replicate of library for A.But if they are three separate biological replicate sample libraries for "A" then you are not going to want to collapse them. You will be losing valuable information.