In comparing mean delta Ct values between treated and untreated samples in RT PCR, what are the statistical tools that you mostly use?

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Nadine A. Gund Popular answer

Hi,

here is a good overview: http://www3.bio-rad.com/B2B/vanity/gexp/content.do?BV_SessionID=@@@@1649667781.1352052928@@@@&BV_EngineID=ccccadfiemfjgeecfngcfkmdhkkdfll.0&root=/Product%20Family/GX/Home&pcatoid=-35468&ccatoid=-36539&country=US&language=English&BV_SessionID=@@@@1649667781.1352052928@@@@&BV_EngineID=ccccadfiemfjgeecfngcfkmdhkkdfll.0

Cheers, Nadine

Nadine A. Gund

mark anthony Carreon

Thank you so much ma'am Gund! Cheers!

Hi, again some literature.

THank you maam! cheers!

Hamsa Tayeb

All samples were collected from patient in their first phase before treated. However, if the patient were completely treated when we take the samples we will not find any RNA to be amplified by RT-PCR

Jorge Valero

I am using the randomization test included in this free software:

http://www.qiagen.com/Products/REST2009Software.aspx?r=8042#Tabs=t1.

I found it hihgly useful.

Nidhi Gupta

you can also check the randomization test included in Bio-rad products

It is quite helpful

Steve Hawley

I found this reference to be pretty useful when I was initally setting up my qPCR calculations:

http://pathmicro.med.sc.edu/pcr/realtime-home.htm

In terms of stats, if you just have one treatment group vs. control, I believe all you need is a simple t-test, which you can do in Excel. If your setup is more complecated than that though, say multiple different treatments, you should perform an ANOVA test, in which case you would need more powerful statistical software. I have been using GraphPad Prism:

http://www.graphpad.com/scientific-software/prism/

which I've found to be pretty user friendly and capable of making publication-quality graphs.

Hugo Murua Escobar

Like Jorge, we are using REST, works fine..

@jorge and @hugo seemingly there are issues encountered running rest on my computer. I really want to try that software. I'm running windows 7 64 bit OS. Ok so i guess t-test is the most appropriate statistical tool. thank you guys for sharing.! cheers.