JoinMap ® List of frequently asked questions

Last modified: 28 September 2010.

1. How do I install my individual license file 'JOINMAP.LIC'?

2. Why do I get the message 'JoinMap is using an evaluation license'?

3. I appear to have problems installing my individual license under Windows 7 or Vista, how do I solve this?

4. Under Windows 7 or Vista I get the successive error messages:

'Access violation at address ... in module 'uxtheme.dll' ...',
'The instruction at ... referenced memory at '0x00000000' ...',
'Runtime error 216 at ...';

what is the problem?

5. Under which versions of MS-Windows runs JoinMap ?

6. I have lost sight of the navigation panel; how do I get it back?

7. Why do I get the message 'insufficient linkage in data to complete the map'?

8. What is the best approach to integrating maps from several populations?

9. How is the modified LOD score calculated for the recombination between two loci?

10. How is the chi-square test for heterogeneity calculated?

11. How do I code loci in a CP population that have two alleles (heterozygous)in one parent and one allele (homozygous) in the other?

12. JoinMap does not accept genotypes 'c' or 'd' in my backcross population (BC1). Why?

13. Against what ratio is tested in the 'Locus genot. freq.' tabsheet with RIx populations?

14. In small data sets JMMAP does not produce a map because it 'Cannot find a first pair to start with.'. Is there a way to work around this problem? (JoinMap 2.0 only)

15. JoinMap says that an output file already exists, and prompts whether to overwrite it. When I say yes, the program aborts with some I/O error. What is wrong here? (JoinMap 2.0 only)

16. What is the procedure to calculate an integrated map from two or more segregating populations? (JoinMap 2.0 only)

17. What is the meaning of the JMGRP-warning: 'number of genes read from loc file is NOT EQUAL to number of genes read from temporary pwd file'? (JoinMap 2.0 only)


1. How do I install my individual license file 'JOINMAP.LIC'?

JoinMap reads its license file 'JOINMAP.LIC' in its program file directory, which is typically 'C:\Program Files\JoinMapX' (X=version number 3 or 4). After installation of the JoinMap software the installed copy of the license file is an evaluation license. Replace that copy with your individual copy, make sure that it is called 'JOINMAP.LIC', and the JoinMap software will become fully functional. Under Windows 7 and Vista this can only be done if you are logged on as a user with 'Administrator' privileges. The easiest way is to start JoinMap from within the installation procedure (by placing the appropriate checkmark in the final screen of the installation), and next use the 'Install License' option of the JoinMap Help-menu.

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2. Why do I get the message 'JoinMap is using an evaluation license'?

When you get this message it means that JoinMap is using a license file 'JOINMAP.LIC' that only allows an evaluation of the software, with limited functionality. When you obtained a individual license file (on your installation CDROM or by e-mail), you must replace this evaluation license file with your individual license file. This individual license file usually has a file name with the extension '.JM4win' (or '.JM3win'). In the replacement of the evaluation license it should become called 'JOINMAP.LIC' (see 1.).

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3. I appear to have problems installing my individual license under Windows 7 or Vista, how do I solve this?

The problem may be caused by the fact that your individual license is installed in the so-called 'Virtual Store', which is a personal 'shadow' copy of protected Windows directories like the 'Program Files' directory. Windows uses the 'Virtual Store' for users without 'Administrator' privileges. You should place your individual license file under the name 'JOINMAP.LIC' in the directory where the executable file 'JoinMap4.exe' resides, which is typically the proper 'C:\Program Files\JoinMap4' directory. This can only be done if you are logged on as a user with 'Administrator' privileges. Make sure that you set the Windows Explorer option to see all file name extensions, otherwise you might think your file is called 'JOINMAP.LIC' whereas in reality it might be called 'JOINMAP.LIC.JM4win' and as such is not found by JoinMap.

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4. Under Windows 7 or Vista I get the successive error messages:

'Access violation at address ... in module 'uxtheme.dll' ...',
'The instruction at ... referenced memory at '0x00000000' ...',
'Runtime error 216 at ...';

what is the problem?

The errors are probably due to the Windows Desktop theme you are using. Some themes appear to be not entirely well programmed and then affect other programs functioning. You can modify your Windows Desktop theme by right-clicking on the Windows Desktop and choosing another theme on the Themes tabsheet.

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5. Under which versions of MS-Windows runs JoinMap ?

JoinMap 4 and 4.1 run under the 32-bit Windows platforms XP, Vista and 7.
They will run as 32-bit software under the 64-bit version of MS-Windows ® 7.
JoinMap 3.0 does not run under Vista and 7, but will run under Windows XP Mode of the Windows Virtual PC.
Windows XP Mode is freely available from Microsoft for Windows 7 Professional or higher.

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6. I have lost sight of the navigation panel; how do I get it back?

Move the mouse pointer to the left edge of the main window where the navigation panel should be. At some point the mouse pointer will change into the dragging shape; if that happens, drag the panel back into sight.
If you have difficulties with this approach, there is an alternative. You should close the program, remove the file 'JoinMap.ProgSetup' in the 'My Documents\JoinMap4' directory, and start the program again; it will restore all view settings of the program.

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7. Why do I get the message 'insufficient linkage in data to complete the map'?

The LOD grouping procedure uses linkage to any single locus already in a group to determine whether that locus belongs to that group. The mapping procedure first has LOD and REC thresholds determining what data are used, and next any marker fitted onto the map during the building process must have at least two distinct links (i.e. links to loci that themselves have r>0, so not r=0, between them) in order to establish a direction in the localization. So if there are not two distinct links due to the stringent thresholds then the program reports that there is insufficient linkage in the data, even though the locus is in the LOD grouping node.
You can set the LOD and REC thresholds for mapping to a lower stringency, so that all information necessary to obtain sufficient linkage will come available.

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8. What is the best approach to integrating maps from several populations?

First, read the previous question and answer about the more technical aspects of how to do this. Generally, the best approach is:
a) calculate maps for each population separately;
b) use fixed orders based on these separate maps to calculate the integrated map; when there are no conflicts between fixed orders, you are ready;
c) when there are conflicts between fixed orders, there are several things you can do to decide which order is the most acceptable:
1) remove the conflicting fixed orders when calculating the integrated map, and see which order is the dominant one;
2) impose the conflicting fixed orders on the separate populations, and see whether these result in acceptable solutions, i.e. reasonable chi-squares and no negative distances;
3) it may be impossible to resolve the conflicts; this can be caused by errors in the data (apply JMCHK), but also by a natural cause, i.e. there is a chromosome inversion. Of course, it is impossible to join maps in the latter case.

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9. How is the modified LOD score calculated for the recombination between two loci?

For each pair of loci a contingency table is produced of the genotypes. The dimensions of the table depend on the population type and the segregation types of the loci (unknown genotypes are ignored). From this table the G statistic (-2 times the logarithm of the likelihood ratio for the Poisson distribution, see e.g. Fienberg, 1979, The analysis of cross-classified categorical data, MIT Press) is calculated to test for independence; the expected number (E) in each cell is calculated from the row-total (R), the column-total (C) and the grand-total (T):

E = R*C/T .


The G statistic then is a summation (SUM) over all cells (O is the observed number, ln() is the natural logarithm):

G = 2 * SUM [ O*ln(O/E) ] .


The G statistic (Gd) has an approximate chi-square distribution with the number of rows in the table minus 1 multiplied by the number of columns minus 1 as the degrees of freedom (d). When the loci have different numbers of genotypes in their segregation, this would present a problem, because this number affects the degrees of freedom in the G test and in the testing of linkage one would need to take account of the degrees of freedom. In order to remove this problem and to ensure the comparability of data coming from different population or segregation types the G statistic with d degrees of freedom, Gd, is transformed approximately to a G statistic, G1, that would have been obtained if there was just a single degree of freedom (as if in a backcross). This approximate transformation is an empirically determined formula (exp() is the exponential function):

e = exp( -Gd/(2*(d-1)) ) ,

G1 = ((4-e)*e - 3)*(d-1) + Gd .


Because in genetics one is used to LOD scores, which are likelihood ratio statistics using the 10-base logarithm instead of the natural logarithm multiplied by -2, the modified LOD score (mLOD) is simply derived from G1:

mLOD = G1 / (2*ln(10)) .

It can be shown that for the case of two loci each segregating in two genotypes (e.g. population types BC1 or DH1) when there is no segregation distortion this mLOD equals the 'normal' LOD score. The modified LOD score is not sensitive to segregation distortion, in contrast to the 'normal' LOD score.

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10. How is the chi-square test for heterogeneity calculated?

From the pwd-file the locus pairs occurring more than once are collected. The pwd-file contains for each pair the recombination frequency and the modified LOD score. In this modified LOD score essentially two important corrections are contained: (1) the segregation data are insensitive to segregation distortion, and (2) the segregation data are transformed as if obtained from a backcross (BC1) under no segregation distortion; this ensures the comparability of data coming from different population or segregation types. For each pair (with two identical loci) the hypothetical number of recombinant (Nr) and non-recombinant (Nn) plants in a backcross (BC1) are calculated based on the recombination frequency (r) and the LOD score (LOD) (r and LOD are read from the pwd-file for each pair) (Nt is the total number of plants, log() is the 10-base logarithm, the numbers Nr, Nn and Nt are treated as 'real's and not as 'integer's):

since:

LOD = Nt*log(2) + r*Nt*log(r) + (1-r)*Nt*log(1-r) ,


we get:

Nt = LOD/(log(2) + r*log(r) + (1-r)*log(r)) ,


and hence:

Nr = r*Nt


and

Nn = (1-r)*Nt.


This way a contingency table is created with for each pair a row with two columns, i.e. the number of recombinants and the number of non-recombinants. From this table the G statistic is calculated to test for independence; the expected number (E) in each cell is calculated from the row-total (R), the column-total (C) and the grand-total (T):

E = R*C/T .


The G statistic then is a summation (SUM) over all cells (O is the observed number, ln() is the natural logarithm):

G = 2 * SUM [ O*ln(O/E) ] .

The G statistic has an approximate chi-square distribution with the number of pairs minus 1 as degrees of freedom. For each pair the contribution to the G test is given in the output, so that it is sometimes possible to locate the most deviant pair.

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11. How do I code loci in a CP population that have two alleles (heterozygous)in one parent and one allele (homozygous) in the other?

Loci heterozygous in one parent and homozygous in the other must be coded as loci with a segregation type <lmxll> or <nnxnp>, depending on which of the parents is heterozygous. The allele in the homozygous parents does not need to be identical to either one of the alleles in the heterozygous parent, genetically these situations are identical.

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12. JoinMap does not accept genotypes 'c' or 'd' in my backcross population (BC1). Why?

In a backcross it is assumed that P1 and P2, the parents of the F1 are fully homozygous. Therefore, as you can see in the following scheme, if a marker is present you are always sure whether the genotype must be 'a' or 'h' in a BC1a (F1 backcrossed to P1), or 'b' or 'h' in a BC1b (F1 backcrossed to P2).

          P1 a  x  P2 b
                  |
                  v
         P1 a  x  F1 h  x  P2 b
               |        |
               v        v
              BC1a     BC1b
  

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13. Against what ratio is tested in the 'Locus genot. freq.' tabsheet with RIx populations?

Loci for which in the data file the classification type is not given, the program tests a:b against the ratio 1:1. Loci for which in the data file the classification type (a,h,b) is given, the program tests a:h:b against the ratio 1:f:1 in which 'f' depends on the generation 'x' given in the RIx code to calculate the expected segregation ratio. In a similar fashion this applies also to classification types (a,c) and (b,d). The classification type can be changed for loci selected in the tabsheet using the Population menu option 'Set X2-Test Classification for Selected Loci'.

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14. In small data sets JMMAP does not produce a map because it 'Cannot find a first pair to start with.'. Is there a way to work around this problem? (JoinMap 2.0 only)

When you duplicate all (!) loci in your loc-file, give the duplicates slightly modified names, and proceed the normal way with jmrec and jmmap, then you get a map with twice as many markers, the duplicates of course completely linked. After removal of the duplicates in the final result, you get your requested map.

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15. JoinMap says that an output file already exists, and prompts whether to overwrite it. When I say yes, the program aborts with some I/O error. What is wrong here? (JoinMap 2.0 only)

The output file probably has a protection, so that the operating system (OS) does not allow you to overwrite this file. Depending on the OS you can change the protection of a file (only when you are the owner) with one of the following commands:

MSDOS:
attrib -r <file name>
SunOS:
chmod u+rw <file name>
OpenVMS:
set prot=(o:rwd) <file name>

When you are not the owner of the file, then you must use another output file name.

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16. What is the procedure to calculate an integrated map from two or more segregating populations? (JoinMap 2.0 only)

First, you must create a loc-file for each population separately. With JMGRP you determine the distribution of the loci over the linkage groups, again for each population separately. Split up, with JMSPL, the loc-files into loc-files for each linkage group and for each population. Calculate with JMREC the pairwise recombination frequencies for each of these files and save them as pwd-files. Now, for each linkage group you must merge, with a text-editor, the pwd-files of the separate populations into one pwd-file, while removing the headers (name=...) (or making comment of them with a ';') of all but the first population. When you have a combined pwd-file for a linkage group, you can feed it to JMMAP and JMMAP will calculate an integrated map. It is advisable to use JMHET to test for heterogeneity in the data, because large differences in recombination frequency between populations can be a problem in map integration.

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17. What is the meaning of the JMGRP-warning: 'number of genes read from loc file is NOT EQUAL to number of genes read from temporary pwd file'? (JoinMap 2.0 only)

The grouping (JMGRP) uses the lower LOD threshold to determine whether locus pairs are to be written to the temporary pwd file. When a locus falls below this threshold for all it's pairs, it will not appear in the temporary pwd file. After the creation of the temporary pwd file all pairs in this file are read and the grouping process is started. JMGRP will notice that loci are not appearing in this temporary file. That's what the warning is about. At the chosen lower LOD threshold such loci are unlinked, and would not appear in any other group.

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