Hello Biostars community,
I'm trying to analyze miRNASeq data of TCGA melanoma (SKCM) samples. This is a prototype analysis in which I picked
hsa-mir-155 and looked at how its expression is correlated with survival. My end goal is expanding this analysis to other cancer types also focusing on other miRNAs.
I performed my analyses with two of the popular packages in R (RTCGA and TCGAbiolinks) and obtained quite different results. I'm trying to make sense of what might be causing the different results. Any help is appreciated. For comparison purposes, I'm attaching some figures and my codes as well.
Overall Kaplan-Meier curves look quite different. These plots were generated on the whole cohort (unsegregated for any parameter). I'm including the plot from
oncoLNC.org database as well for comparison purposes. RTCGA looks more like the
You can see similar differences when the data is segregated based on
When I segregate patients based on the expression of
hsa-mir-155 (top and bottom thirds), the differences become more obvious:
To understand what might be different in the datasets I exported the data from both packages and performed a comparison. Linked excel file shows the comparisons including clinical details (
days_to_last_follow_up) and gene expression values of
reads_per_million_miRNA. I noticed that there are considerable differences between two datasets. I'm pretty sure, the way I organized the data is ok and I don't think the differences are due a mistake in data manipulation in R.
Please let me know why you think there is a discrepancy here. I'm pretty new to this type of analyses and hopefully, I didn't miss something silly.
Thank you very much in advance for your insights,