I have done a genetic association analysis based on SPSS software. The allelic association has come out as a significant association. But when I wanted to compute the odds ratio in both allelic and different genotypic models based on cross-tabulation, the SPSS showed the odds ratio of control/case instead of case/control. Can I report this ratio in scientific journals? For better clarity, one SPSS file is attached below. Any suggestion will be appreciated. The analysis process is mentioned briefly below.
> Denote control 1 and case 2 in SPSS. Also denote AG, GG genotype 1, and AA genotype 2 in SPSS (Dominant model).
> Import the excel sheet in SPSS.
> Go descriptive stat, click crosstab.
> Put population (case and control column) into row and genotype into the column.
> Select chi-square, percentage, and risk.
> Continue
Case/control= 1/(control/case) is an.identity.that should solve your problem. Best wishes David Booth
BTW SPSS doesn't know what your labels stand for but presumably you do.
As always you need to know what you are doing, as SPSS does not. By default it uses the highest coded category as the base or reference. This can be changed.
@Prof. Jones, why isn't my identity a simple approach to doing just what you said. My SPSS problem has always been I can't understand the SPSS documentation. This seems to be the case again. As I understand the question my approach should work as long as one knows which is case and which is control. Best wishes David Booth
Thank you so much. If I mention the odds ratio as control/case what I got from SPSS in the scientific journal, will it be a problem? Can I describe as " the control group has XX times more prevention from the disease than the disease group"?
If I calculate 1/(control/case) the odds ratio, then how can I calculate the 95% CI?
David Eugene Booth , no problem with your approach, my issue is with SPSS, see this on how you have to change to syntax to get another category as the base:
https://www.ibm.com/support/pages/can-i-specify-reference-category-other-first-or-last-spss-binary-logistic-regression
so arbitrary.
Further to what Kelvyn Jones said, if one wishes to use CROSSTABS to compute an OR for Cases relative to Controls, then the group variable must be coded such that Case code < Control code.
* Reproduce the result in the original post.
* Denote control 1 and case 2 in SPSS.
* Also denote AG, GG genotype 1, and
* AA genotype 2 in SPSS (Dominant model).
NEW FILE.
DATASET CLOSE ALL.
DATA LIST LIST / Group gtype (2F1) n (F5.0).
BEGIN DATA
1 1 58
1 2 298
2 1 35
2 2 85
END DATA.
VARIABLE LABELS gtype "Genotype".
VALUE LABELS
Group 1 "Control" 2 "Case" /
gtype 1 "AA,GG" 2 "AA".
WEIGHT by n.
CROSSTABS Group by gtype / STATISTICS= RISK.
****************************************************.
* If you want to use CROSSTABS to get the OR for
* Cases relative to Controls, you must recode
* the Group variable so that Case code < Control code.
****************************************************.
RECODE Group (1=2)(2=1) INTO grp.
FORMATS grp (F1).
VALUE LABELS grp 1 "Case" 2 "Control".
CROSSTABS
TABLES Group by gtype /
TABLES grp by gtype / STATISTICS= RISK.
* If you use GENLIN to estimate a logit model,
* you can specify reference categories for both
* the explanatory variable and the outcome variable.
EDIT. Note that the last CROSSTABS command above can be simplified as follows:
CROSSTABS Group grp by gtype / STATISTICS= RISK.
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