Dataset: ROSMAP_arrayExpression.tsv Synapse ID: syn4009567 In this file, there are columns starting with ?Detection??, eg, Detection.MAP_50100220, I am wondering if this indicates the detection P value of this probe or the Th value. If it was detection P value, the P value looks larger than expected, as most of probes have detection P value over 0.05 in samples. That being said, these probes might be excluded in the preprocess. I guess this value might be the value of 1-detection P value. But not sure. Could you please help with this matter? Thanks

Created by Zuyun Liu Zuyunliu
Indeed, your inference about 1-pval sounds plausible to me, especially as the final list is similar using that.
Thanks for the replies. I may say what I guess before is correct. That being said, the Detection Value provided in Dataset: ROSMAP_arrayExpression.tsv might be the value of 1 - detection P value, most of them around 0.95. Therefore, I could use this value to filter the probes now. The final list looks reasonable. What makes this happen might be due to the different versions of Illumina softwares/R packages (minfi). It seems like the older and new ones provide different values but the principle is the same.
Thank you for bringing this to my attention, Mette. I don't recall using this matrix, but I was essentially handed some expression values and modules, which would have been produced after this point, so perhaps Bin will know about this, or who processed it?
Hi @CINDERellA. Is this something you can help answer? See question above related to the ROSMAP array data
Thanks Mette, I checked that paper but still cannot get my answer. Some details were missed but are important for me to clean the whole array. Zuyun
This study has been described in more detail in this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3677161/#SD1. Let us know if that provides you with your answer

Gene expression data issue in syn4009567 (ROSMAP_arrayExpression.tsv) page is loading…