Entering edit mode
7.6 years ago
yjliu1127
•
0
Hi everyone,
I have one question about the command line for assigning conditions in DESeq2. The following are the count table I got. I want to assign WT6A, WT6B and WT6C as controls (3 replicates) and KO6A, KO6B and KO6C (3 replicates) as treated samples. column 1 is the gene name. column2-4 will be controls and column5-7 will be the treated samples.
- WT6A WT6B WT6C KO6A KO6B KO6C
- dnaA 6594 7412 3401 9067 7344 3803
- dnaN 4274 5048 3680 7368 7300 6571
How should I write the command line for this?
Thanks, Yong
Do you already have everything in a single file or data.frame? If so, see
help(DESeqDataSetFromMatrix)
.Thanks Ryan! I'm really bad at coding. I checked the website. I still cannot figure out. My experiment is pretty straight forward. It's two-group comparison between control and treatment. Each group has 3 replicates. This is the code I typed in R:
However, there is an error: Error in data.frame(row.names = c("WT6A", "WT6B", "WT6C", "KO6A", "KO6B", : row names supplied are of the wrong length.
Could you please let me know how to fix this problem?
The "group" part is redundant and was producing a vector of length 18 (rather than 6) anyway, due to having an extra 3 in there.
Thanks! I have another mistake in the code.
How can I fix this? and How can I set the control group as the basal level if I want to compare treated samples with control samples? Is the following code right?
Thanks a lot!
The control group is already the base level, "control" is lexicographically before "treated".
The error is due to there being non-integer values in
countMatrix
. Figure out what that is and fix it.Thank you very much! Yong