Software For Analysing Real-Time Pcr Data

Question

[Khader Shameer]

To validate the hits from microarray experiment, we have done RT-PCR experiment using Roche LightCycler 480. We would like to analyze this data using a free software. I know about the QPCR but installing them locally may create issues as it is tightly integrated with JBOSS and PostgreSQL. I already have Apache and MySQL in my server and I only need to run QPCR for few genes. Installing it locally doesn't seems to be worthy. Wondering if there is any other webserver or package or module for analyzing the Real-Time PCR data.

[Nicojo]

You should use RT-PCR for Reverse Transcription PCR, qPCR for Real Time PCR and RT-qPCR for Reverse Transcription Real Time PCR. For anyone doing qPCR, I'd recommend to follow the MIQE guidelines (http://www.gene-quantification.de/miqe.html ;)

[Nicojo]

So far I've only used the instrument's software, mostly visualize and then to export the data. Then I use Prism to play with the numbers...

[Khader Shameer]

Thanks for your suggestion. I will go through the MIQE guidelines. Have installed QPCR locally or used the QPCR server or at Graz ?

[Khader Shameer]

Thanks for your suggestion. I will go through the MIQE guidelines. Have you installed QPCR locally or used the QPCR server at Graz ? – Khader Shameer

[Nicojo]

Please let us know what you think of CAmpER once you've had a chance to test it!

Answer 1

[Khader Shameer]

Now, I am using an R/BioC package for qPCR data analysis. LC480 based Cp values can be imported using some changes in file format. I got exceptional help and input from the authors of the HTqPCR and the package is quite efficient, implements 4 normalization methods and several other advanced analysis routines for qPCR data analysis. Highly recommended. Links to HTqPCR at BioC and HTqPCR Paper

We are currently using a vendo supported software DataAssist from Life technologies for the analysis of qRT-PCR.

Answer 2

[Rm]

ExP€Rt: A Tool for Automated qPCR Data Analysis

It's simple to use and can handle multiple housekeeping normalizers and a Calibrator (control) sample:

Another one: A new mathematical model for relative quantification in real-time RT-PCR.

Answer 3

[Michael]

A former colleague has developed the CAmpER web-application for exactly that and as an alternative to the instruments software. Provides some algorithms for calculation of amplification efficiencies and crossing points, in addition to what the vendor software provides and has also an integrated lims.

login: http://camper.cebitec.uni-bielefeld.de/cgi-bin/camper_login.cgi

I think there is now an open test-project, otherwise you can ask the author, to get your own account.

[Khader Shameer]

I have written to the author of CAmpER for a user account.