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marasodi
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@marasodi-15998
Last seen 6.5 years ago
Hi
Im am doing a project on RNA Seq, and will like to check differentially expressed genes. The data is between 2 genotypes, at 4 time points, treated and untreated samples all in 3 replicates. How do I go about such data because I'm not sure as to whether what I'm doing is right.
| ids,"Subject","Time","Genotype","Subject" |
| AC1_14d,"R2","336","A","C2" |
| AC1_24h,"R2","24","A","C2" |
| AC1_48h,"R2","48","A","C2" |
| AC_14d,"R1","336","A","C1" |
| AC1_7d,"R2","168","A","C2" |
| AC2_14d,"R3","336","A","C3" |
| AC2_24h,"R3","24","A","C3" |
| AC2_48h,"R3","48","A","C3" |
| AC_24h,"R1","24","A","C1" |
| AC2_7d,"R3","168","A","C3" |
| AC_48h,"R1","48","A","C1" |
| AC_7d,"R1","168","A","C1" |
| AR1_14d,"R2","336","A","T3" |
| AR1_24h,"R2","24","A","T3" |
| AR1_48h,"R2","48","A","T3" |
| AR_14d,"R1","336","A","T3" |
| AR1_7d,"R2","168","A","T3" |
| AR2_14d,"R3","336","A","T3" |
| AR2_24h,"R3","24","A","T3" |
| AR2_48h,"R3","48","A","T3" |
| AR_24h,"R1","24","A","T1" |
| AR2_7d,"R3","168","A","T3" |
| AR_48h,"R1","48","A","T2" |
| AR_7d,"R1","168","A","T2" |
| BC1_14d,"R2","336","B","C2" |
| BC1_24h,"R2","24","B","C2" |
| BC1_48h,"R2","48","B","C2" |
| BC_14d,"R1","336","B","C1" |
| BC1_7d,"R2","168","B","C2" |
| BC2_14d,"R3","336","B","C3" |
| BC2_24h,"R3","24","B","C3" |
| BC2_48h,"R3","48","B","C3" |
| BC_24h,"R1","24","B","C1" |
| BC2_7d,"R3","168","B","C3" |
| BC_48h,"R1","48","B","C1" |
| BC_7d,"R1","168","B","C1" |
| BR1_14d,"R2","336","B","T2" |
| BR1_24h,"R2","24","B","T2" |
| BR1_48h,"R2","48","B","T2" |
| BR_14d,"R1","336","B","T1" |
| BR1_7d,"R2","168","B","T2" |
| BR2_14d,"R3","336","B","T3" |
| BR2_24h,"R3","24","B","T3" |
| BR2_48h,"R3","48","B","T3" |
| BR_24h,"R1","24","B","T1" |
| BR2_7d,"R3","168","B","T3" |
| BR_48h,"R1","48","B","T1" |
| BR_7d,"R1","168","B","T1" |
Thanks in advance
This support site is intended to help people who have particular questions about how to use Bioconductor software, rather than as a place where people will explain how to do an entire analysis. There is a vignette for ballgown (as there are for all Bioconductor packages) that is intended to help people get started. Have you read that?
If you have particular questions, feel free to ask, but do note that you need to be more explicit. All you have said thus far is that you have some data and you want to use ballgown. That isn't enough for anybody to help. What did you try? What happened? Why do you think you might be wrong?