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First off, thank you for all of the awesome work with GTEx v8. I am trying to compare my eQTL results to the v8 GTEx database (see which eQTLs are replicated vs novel to my cell type).
I am thinking it would be optimal for me to compare my eQTLs with q-value < 0.05 to the *.signif_variant_gene_pairs.txt.gz files, however, am struggling to find (or derive) q-values for each of these variant-gene pairs in GTEx: https://gtexportal.org/home/datasets
The *.allpairs.txt.gz files only contain pval_nominal.
The *.signif_variant_gene_pairs.txt.gz files contain adjustments through pval_beta. Since pval_beta tends to exceed 0.05 in these files, I assume that this list of "significant variant-gene pairs" was the subset of *.allpairs.txt.gz with 'qval' ≤ 0.05, however, there is no qval column?
The *.egenes.txt.gz files contain adjustments through qval.
I am confused as to why qval isn't included in all 3 file types. Given that the "eGenes are the rows with qval ≤ 0.05," I assume I should be using qval to identify which eQTLs replicate between my analysis and GTEx. It would be really helpful if the *.allpairs.txt.gz files contained a qval column for this comparison (or code for which I could derive the qval column?). At first I tried to do qvalue(pval_beta) for the subset of significant variant-gene pairs, but this fails to replicate the qval values since it is a subset of the variant-gene pairs.
Thanks in advance for any help you might be able to provide,
Chris
The text was updated successfully, but these errors were encountered:
FDR was computed at the gene level (to identify eGenes), and therefore the q-values are only present in the *.egenes.txt.gz files. For details, please see Section 4.2 of the supplementary materials for additional details.
The *.signif_variant_gene_pairs.txt.gz files contain all pairs that pass the significance threshold for each eGene.
To test replication, consider computing the pi1 statistic (Section 5 of the supplementary materials). For that, you only need the nominal p-values (from the *.allpairs.txt.gz files) in GTEx corresponding to the variant-gene pairs that you're testing for replication.
Thank you very much for your helpful reply. This clarifies many of the things I was confused about. I will give this a try and let you know if I get stuck.
Hi,
First off, thank you for all of the awesome work with GTEx v8. I am trying to compare my eQTL results to the v8 GTEx database (see which eQTLs are replicated vs novel to my cell type).
I am thinking it would be optimal for me to compare my eQTLs with q-value < 0.05 to the
*.signif_variant_gene_pairs.txt.gz
files, however, am struggling to find (or derive) q-values for each of these variant-gene pairs in GTEx:https://gtexportal.org/home/datasets
As I understand the documentation from:
https://storage.googleapis.com/gtex_analysis_v8/single_tissue_qtl_data/README_eQTL_v8.txt
the order of p-value adjustment follows the path of:
pval_nominal -> pval_perm -> pval_beta -> qval
In the files I see:
*.allpairs.txt.gz
files only containpval_nominal
.*.signif_variant_gene_pairs.txt.gz
files contain adjustments throughpval_beta
. Sincepval_beta
tends to exceed 0.05 in these files, I assume that this list of "significant variant-gene pairs" was the subset of*.allpairs.txt.gz
with 'qval' ≤ 0.05, however, there is noqval
column?*.egenes.txt.gz
files contain adjustments throughqval
.I am confused as to why
qval
isn't included in all 3 file types. Given that the "eGenes are the rows with qval ≤ 0.05," I assume I should be usingqval
to identify which eQTLs replicate between my analysis and GTEx. It would be really helpful if the*.allpairs.txt.gz
files contained aqval
column for this comparison (or code for which I could derive theqval
column?). At first I tried to doqvalue(pval_beta)
for the subset of significant variant-gene pairs, but this fails to replicate theqval
values since it is a subset of the variant-gene pairs.Thanks in advance for any help you might be able to provide,
Chris
The text was updated successfully, but these errors were encountered: