Here's the GeNorm excel sheet so you don't have to bother trying to learn python. Also attached GeNorm manual and a couple other excel methods (NormFinder and BestKeeper), an example for how to input data for NormFinder (I have nothing for BestKeeper, sorry) and the seminal papers for all 3 algorithms in case you were interested in the nitty gritty.

Perhaps this link will help

http://download.gene-quantification.info

I don't have the link handy, but there is a python library named "eleven" that implements the geNorm algorithm. Should be findable online with a search. 

P.S. found it - https://pypi.python.org/pypi/eleven

Thanks Vincent and Michael..the link to phyton libraray is available..on genequantification.info..but I would prefer using excel sheet...

Well, as explained here - http://medgen.ugent.be/~jvdesomp/genorm/ the old excel sheet is no longer distributed so you may find it impossible to download from anywhere.  You could try using the free 15 day trial of gbase+ (linked to from that site).

I think the BioConductor package NormqPCR also implements the geNorm algotithm in R.

Good suggestion from Evelyze

Thanks Michael, Evelyze, and Vincent. The website seems to be most convenient and comprehensive, I will start with it. 

I started using the web site suggested by Evelyze. Unlike the software I used previously, it doesn't provide the combinations evaluation automatically....To get the combination values, I calculated the values for geometric means of the combination, and put them as a reference gene, Is this the way for evaluating combinations, or Genorm Algorithm has a different formula for evaluating combinations?? 

Here's the GeNorm excel sheet so you don't have to bother trying to learn python. Also attached GeNorm manual and a couple other excel methods (NormFinder and BestKeeper), an example for how to input data for NormFinder (I have nothing for BestKeeper, sorry) and the seminal papers for all 3 algorithms in case you were interested in the nitty gritty.

Brandon, thank you for the files!

I was looking for some of those during the last couple months!

Have you checked in your assays if the results on the different platforms are similar?

I have not had the chance to cross-check any of them, unfortunately. Sometimes, they do give different answers, so it may be best to do all 3 and do a final ranking based on the geometric mean of each reference gene candidate's scores from all 3 algorithms. There's also a website that can do just that for you: http://www.leonxie.com/referencegene.php#

Fantastic!

Thanks, Brandon!

Thanks :)

Thanks so much!

You can try our new LEMming tool, described here:

LEMming: A Linear Error Model to Normalize Parallel Quantitative Real-Time PCR (qPCR) Data as an Alternative to Reference Gene Based Methods

Article LEMming: A Linear Error Model to Normalize Parallel Quantita...

Leonxie webpage is not available since July: http://www.leonxie.com/referencegene.php#

Do you have an alternative? This site was very useful to choose the best reference gene.

Have you found any alternative to http://www.leonxie.com/referencegene.php# ? @ Alejandro Ibáñez-Costa ·If yes please share here, Thanks

Thanks Maria, Alejandro, and Zeeshan

RefFinder apparently got moved here: http://fulxie.0fees.us/?type=reference

Thanks Ralf

Dear Jamila,

The leonxie.com link seems to be defunct. Apparently, this one is the new one:

http://fulxie.0fees.us/

It should not require you to download or install anything as it is an online webtool.

EDIT: 2018-10-25 The above link and http://leonxie.esy.es/RefFinder/ are not working anymore either, but this seems to work:

http://150.216.56.64/referencegene.php

I just checked the RefFinder, seems like a handy tool. But it looks like you can only insert the raw Cq values and no efficiencies. That would mean in the case of different efficiencies of your primer pairs, the calculation of the stability values would be flawed.

What do you think about that?

Hi @Jorg Panzer, I have also just used RefFinder for the first time, having given up on BioGazelle/geNorm, and am very happy with the results!  I generated my Cq data in LinRegPCR from the "raw" Rn data off the pcr machine. LRP calculates the exact efficiency of each individual well, and analyzes the mean efficiency per target/amplicon/gene. You can use the individual efficiency, or the mean in your post-analysis. It also sets a threshold for each, and then calculates the Cq. I would think this is more accurate than running the efficiency separately (as you are talking about). At any rate, that's what I'm doing.  LRP is very easy to use.  Its real goal is to back-calculate the pre-amplification concentration of a sample (N0), and to use those numbers to calculate relative expressions, but you can use the Cq values to calculate ddCt (the numbers from both analyses are very similar, in my experience, IF you use the Cq LRP generates.  My only two complaints is that you have to generate your errors independently - it doesn't calculate that for you, and if you are dealing with multiplate data, it gets a little complicated to compare between them, but the authors have a recommendation to compile the data in the FAQ section. 

the software download, FAQ and manual:

http://www.hartfaalcentrum.nl/index.php?main=files&sub=LinRegPCR

a youtube tutorial:

https://www.youtube.com/watch?v=Gkq0g_6OYQM

Cheers.

Thank you Amy! I will check it out and tell you what I think about it.

Thanks Kamran

As described on the original geNorm page (https://genorm.cmgg.be/), the XLS-sheet is no longer available for download.  However, a much improved geNorm module is integrated in qbase+:

• fully automatic and expert result report
• handles missing data
• single best reference gene identification
• much faster

A free version for two weeks can be requested on the qbase+ website.

https://www.qbaseplus.com

Thanks Ward but how much is it after the two weeks ;) ?

That information is also available on the website. Nevertheless, 2 weeks is enough for some people.

Ok, thanks Ward

Hello everyone, the link of RefFinder got there : http://leonxie.esy.es/RefFinder/

Enjoy!

Dear Brandon Hendrix

genorm excel sheet is opening as blank in windows 10. Nothing is there

If you are still looking for the links, I've posted a new link to RefFinder that uses geNorm in another post, it's free to use, here it is: https://www.heartcure.com.au/for-researchers/

Nishat Sarker

Thanks

i cant open the NormFinder excel file

NormFinder:

Microsoft Visual Basic

Run-time error '5':

Invalid procedure call or argument

and when i try to insert the column and row in geNorm Excel, it shows:

Compile error:

Can't find project or library

(Mod_Intro 37:11)

Anyone experiences the same things?

and what should i do to open the file to run the test?

try this:

http://fulxie.0fees.us/

Dear Terry Lee , thanks alot sharing this webpage with RefSeq, just one question, Do you know the data format to put into the data window? There are not any guide to follow, just an example, which data seem not to be Ct values? Any Help will be great. Thanks in advance.

Carlos Gaete-Eastman they are Ct values. If I recall, it's a simple tab-delimited file with the different reference genes that were tested as columns labeled across the top row, and the their reported Ct values for each sample in the rows below. The example looks messy because of the tab spacing. Your data can be organized in Excel or any spreadsheet or even basic text file very easily, before pasting into the website.

Thanks Terry Lee for sharing RefFinder link. It's super handy. Just dump all the CT value (regardless of the subject group) of each HK gene. See example below:

B-actin B2M Gapdh Hprt1 TBP

20.65 21.28 20.90 26.63 21.48

20.73 21.26 20.93 26.64 21.44

20.89 21.78 21.08 27.17 21.64

20.84 21.80 21.03 27.07 21.73

21.30 21.67 21.06 26.86 21.58

20.92 21.60 21.05 26.97 21.73

RefFinder will rank the HK genes based on their stability across each subject group.

Enjoy