Issues with PRACTICAL prostate cancer data

[nabilakazmi]

Hi there,

I am aware that overall PC data has been reformatted but If I compare the summary data of rs13107325 to what I had about a year ago and now, the actual value of beta and se are changed. Please see below

Overall prostate cancer (old) SNP beta se pval eaf effect_allele other_allele
rs13107325 0.0122 0.0158 0.4382 0.9255 C T

Overall prostate cancer (now) SNP beta se pval eaf effect_allele other_allele rs13107325 -0.0148 0.0163 0.3647 0.0684 T C

Also, in advanced prostate cancer rs13107325 has two rows and I think because the snp is tri-allelic but then why the beta and se are exactly the same as you can see below: SNP beta se pval eaf effect_allele other_allele rs13107325 -0.0089 0.0284 0.755299 0.0686 A C rs13107325 -0.0089 0.0284 0.755299 0.0686 T C

Thank you for your help.

[mightyphil2000]

Hi Nabila

What are the IDs for the two datasets?

This is what it looks in the original results files:

overall prostate cancer (this matches the current version): MarkerName Allele1 Allele2 Freq1 FreqSE MinFreq MaxFreq Effect StdErr P-value Direction 4_103188709_C_T t c 0.0684 0.0041 0.0558 0.0784 -0.0148 0.0163 0.3647 -++---+-

I'm still investigate the advanced prostate cancer results. But I can confirm the duplicate is not present in the original results file.