Download TMP values for all samples

[Andy Phillips]

Hi,

I'm enjoying using the 3D RNA-seq app for my wheat data and appreciate the simple workflow. However, I would like to be able to extract the normalized TPM values for all genes and all samples (or possibly means and SD across reps). I expected to find this in the "Results" section of the working directory (I'm running 3D RNA-seq locally in RStudio) but it doesn't seem to be there - only the DE testing statistcs and similar. Is it possible to extract the TPM data from the analysis?

Thanks,

Andy

[wenbin guo]

Hi, 

"Normalized" TPM is not availabel in the output. But, in the "Result" folder, it should include files of Gene TPM.csv and Transcript TPM.csv. These are the TPM values before normalisation. You can use these data to calculate the mean and sd of TPMs across different conditions. If you can't find the TPMs in the "Result" folder, you can get from the txi_genes and txi_trans objects after the tximport step. The TPMs can be extracted from txi_genes$abundance and txi_trans$abundance. 

[Andy Phillips]

Thanks Wenbin, I see them now - I was looning in the wrong temporary app folder.

Cheers, Andy