microRNA PCR analysis

Question

[anjasta47]

Hi all, I am currently performing an analysis of microRNA RT-PCR data. The analysis was performed using miRCURY LNA miRNA Custom PCR Panel (Qiagen). The miRNA expression was performed for 31 miRNAs. Among them, three miRNA were used for miRNA expression normalization. This project is based on one of the previous analysis performed at my department. I have already performed data normalization and would like to perform differential expression analysis. However I only have some experience in performing differential expression on raw reads from NGS. Here I received Ct values. Could somebody please help me and suggest the best way to analyze this data. Which R package to use? I would like to preform differential expression and do volcano plots. I am looking for a possibly simplest way since my main profession is other that being a bioinformatician. Could someone please give me a hand at this? All tips are welcomed.

[cpad0112]

There are few R packages for qPCR like Readpcr, HTqPCR, NormqPCR that take ct values and analyze the data. Try them.

Answer 1

[Eugene A]

It seems that just need to perfrom the statistical comparison between each individual miRNA for these two condition. Select a test according to your sample size (how many mesurments you have for each condition). Most likely u test or t test will work for you