Dear all, I was wondering if the available files in syn18103849 include the following analysis: "All analysis used log2 counts per million (CPM) following TMM normalization implemented in edgeR (v3.22.5). Correction for GC content bias was performed with cqn (v1.26.0). Genes with over 1 CPM in at least 50% of the experiments were retained" ( If not, how should I use the gene expected counts and gene length for an eQTL analysis. Thank you.

Created by Diana Prata dmprata
I would like to make a follow-up question regarding the analysis of the data. There is a folder with the normalized expression values corresponding to the data from release 1.0 in syn3280464. Are there similar files corresponding to the data from release 3? I could only find the quantitated expression, syn18103849, which contains the expected gene counts and the gene lenghts, but does not contain the normalized expression values. According to the manuscript with the description of the data from Release 3, the analysis consists in an adjustment using CPM following the TMM normalization implemented in edgeR. Could you guide me to the files that contain those normalized expression values? Thank you very much.
Yes, it is the data described in this manuscript:
The paper you are referring to is the one I cite above? If otherwise, would please guide me to the paper link? Thank you very much.
The data from release 3 is the data described in the Scientific Data paper. Let me know if that answers the question

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