How to use the TaqMan2Results macro:


This macro allows you to transfer your data from output TaqMan files into your results file. 
This macro also offers the possibility, if you want, to compare the Taqman data for a batch of plates, read by two different operators. 
If you choose to read a batch of files, from two different users, 
you have to create two different folders, containing TaqMan files read by each user, for the same batch of samples.
Then the macro will ask you for the two folders.
Notice that the macro will process all files contained in  folders. 
Make sure you have only plate files you want to be processed by the macro.

Its use is very easy : 
Open the two plate files (first and second reading)  : 
You have to select the folder containing the first batch of TaqMan output files (i.e., read by the first operator)
You have to select the folder containing the second batch of TaqMan output files (i.e., read by the second operator)
Make sure that the format requirements are met.
Here is an example of a properly formatted file:

SDS 2.1	AD Results	1							
Filename	plate EGA 011 SD 28R.sds								
PlateID	EGA011ABCD								
Assay Type	Allelic Discrimination								
Run DateTime	1.12.2004 15:37								
Sample Information									
Well	Sample Name	Marker Name	Allele X Rn	Allele Y Rn	Call	Quality Value	Call Type	Task	Passive Ref
1	72524917	D28235.5209-TG	0.6098798	1.6452396	D28235.5209T	100	Manual	Unknown	751.8816
2	52599260	D28235.5209-TG	1.3060224	1.7955936	Both	100	Manual	Unknown	758.2848
3	51245630	D28235.5209-TG	0.64102083	2.4226325	D28235.5209T	100	Manual	Unknown	748.478
4	61090237	D28235.5209-TG	0.6027125	2.362953	D28235.5209T	100	Manual	Unknown	738.2897
5	61112874	D28235.5209-TG	0.6457324	2.3387187	D28235.5209T	100	Manual	Unknown	776.40015
6	41184101	D28235.5209-TG	0.6802159	2.4564142	D28235.5209T	100	Manual	Unknown	814.0498
7	22311900	D28235.5209-TG	0.69056743	2.2290199	D28235.5209T	100	Manual	Unknown	975.38293
8	24679869	D28235.5209-TG	0.67194396	2.4190805	D28235.5209T	100	Manual	Unknown	954.5143
9	72541050	D28235.5209-TG	0.6805688	2.3868046	D28235.5209T	100	Manual	Unknown	978.71576
10	61164158	D28235.5209-TG	0.67691207	2.2822857	D28235.5209T	100	Manual	Unknown	993.2296
11	51262140	D28235.5209-TG	0.6931439	2.2600842	D28235.5209T	100	Manual	Unknown	1084.5939
12	NTC	D28235.5209-TG	0.6056874	0.8465618	NTC		Manual	NTC	1369.3849
13	72526102	D28235.5209-TG	0.6425953	2.4029582	D28235.5209T	100	Manual	Unknown	1290.3566
14	52599460	D28235.5209-TG	0.71323776	2.7292786	D28235.5209T	100	Manual	Unknown	1296.0095
15	Qc_51247550	D28235.5209-TG	0.8926737	2.5935225	D28235.5209T	100	Manual	Unknown	1463.4194
16	61090531	D28235.5209-TG	1.4384847	2.1995547	Both	100	Manual	Unknown	1429.958
17	61113711	D28235.5209-TG	0.6696649	2.557972	D28235.5209T	100	Manual	Unknown	1383.3431
18	41183497	D28235.5209-TG	0.69521827	2.5697856	D28235.5209T	100	Manual	Unknown	1509.0962


Note that the whole marker name should be composed by the marker name (no special format for this)  followed by the two alleles. 
Only one letter is authorized per allele. 
The two last letters will be interpreted by the macro as the alleles.
If you have to genotype insertion or deletion, please use the "I" or "D" letters. 
When you define the detectors in SDS,  
please make sure that the last character corresponds to one of the alleles.
(the same letters as the ones chosen in the marker name).
Next, open your results file.
An example of properly formatted results file is available here:

MyStudy Plate Row Column D28235.5209-TG SNP002-AG SNP003-TC
MyStudy  -  -   T/G A/G T/C
72524917 EGA011ABCD A 1      
52599260 EGA011ABCD A 2      
51245630 EGA011ABCD A 3      
61090237 EGA011ABCD A 4      
61112874 EGA011ABCD A 5      
41184101 EGA011ABCD A 6      
22311900 EGA011ABCD A 7      
24679869 EGA011ABCD A 8      
72541050 EGA011ABCD B 1      
61164158 EGA011ABCD B 2      
51262140 EGA011ABCD B 3      
AND SO ON...            


Once you have selected the TaqMan Files and you results files, 
push the button "Data Transfer".
If you've chosen the double reading, 
check for discrepancies, in the column "Consensus",  that may exist between the two readings and correct them.
To save time, you can press the button "Solve discrepancies" . 
This will replace all of them by a "-" character, meaning undetermined genotype. 
Once you have resolved all discrepancies, push the button "TaqManTo Results".
If the marker name is not in the results file, the macro will add it for you.
If you add some results for a previously processed marker,
the macro will add new results to the corresponding samples, in the proper column.

At the end of the transfer, you will be prompted to do the Quality Control analysis. 
If you choose "Yes", make sure you have added the "Qc_" to the sample names beforehand.
The macro will know that samples whose name starts with "Qc_" are quality control samples,
and it will compare the genotype found for the sample and the genotype found for its control.
Any discrepancies will be recorded in the "Quality Control Report File", a text file created during the analysis.

Finally, you can translate the genotypes, recorded in the results file in nucleotides "A", "T", "C", "G"  
into numbers "1", "2", "3", "4".
The translation will be recorded in a new worksheet "Translation", added during the process in your results file.

Description of the macro.

Download the macro.

Back to the program list.

This page was last updated on: July 01, 2005 by Stéphanie Monnier