Confusion from forestPlot

[beginner984]

Hi

Sorry whatever I try to get the logic of forestPlot I fail. What are you putting into the odds ratio? I can see this as odds of having the PML gene, but odds ratio has me confused. Why odd ratio is negative (apart from taking log)

Thank you for any help

[PoisonAlien]

Hello, Odds ratios are from Fishers exact test estimated from mafCompare function.

> pt.vs.rt <- mafCompare(m1 = primary.apl, m2 = relapse.apl, m1Name = 'Primary',
                       m2Name = 'Relapse', minMut = 5)
> pt.vs.rt
$results
   Hugo_Symbol Primary Relapse         pval         or       ci.up      ci.low      adjPval
1:         PML       1      11 1.529935e-05 0.03537381   0.2552937 0.000806034 0.0001376942
2:        RARA       0       7 2.574810e-04 0.00000000   0.3006159 0.000000000 0.0011586643
3:       RUNX1       1       5 1.310500e-02 0.08740567   0.8076265 0.001813280 0.0393149868
4:        FLT3      26       4 1.812779e-02 3.56086275  14.7701728 1.149009169 0.0407875250
5:      ARID1B       5       8 2.758396e-02 0.26480490   0.9698686 0.064804160 0.0496511201
6:         WT1      20      14 2.229087e-01 0.60619329   1.4223101 0.263440988 0.3343630535
7:        KRAS       6       1 4.334067e-01 2.88486293 135.5393108 0.337679367 0.4897762916
8:        NRAS      15       4 4.353567e-01 1.85209500   8.0373994 0.553883512 0.4897762916
9:      ARID1A       7       4 7.457274e-01 0.80869223   3.9297309 0.195710173 0.7457273717

$SampleSummary
    Cohort SampleSize
1: Primary        124
2: Relapse         58

In the above list results contains details about fishers output. Simple way to interpret the first row is that the odds of observing PML gene in Primary APL is quite low (0.03 times than in relapse). Similarly, 4th row, odds of observing FLT3 in primary is quite high (3.56 times more likely than in relapse). These are the values plotted in forestplot on log10 scale. Hope this helps.

[beginner984]

Thank you very much

Quite explanatory

In my case

Likely I have the same number of observed NAV3 in both groups but I have a odds of observing NAV3 in M1 group (that is why log odd ratio is positive); But why when I have the same number of observations?

[PoisonAlien]

7 out of 94 is significantly different from 7 out of 31

[beginner984]

Apologise @PoisonAlien

I have compared two mafs

> head(pt.vs.rt$results)
   Hugo_Symbol Responders NonResponders        pval       or      ci.up   ci.low   adjPval
1:        NAV3       0       8 0.007407514 0.000000  0.6570311 0.000000 0.1708848
2:        TPTE       5       0 0.013670784      Inf        Inf 1.254574 0.1708848
3:      AHNAK2       9       3 0.025101015 4.879954 31.1648231 1.063497 0.1915460
4:       ERBB4       0       6 0.030647360 0.000000  1.0033597 0.000000 0.1915460
5:      GABRA4       0       5 0.061822725 0.000000  1.3189994 0.000000 0.2575947
6:       KCNQ3       0       5 0.061822725 0.000000  1.3189994 0.000000 0.2575947
>

The results says that ERBB2 has been mutated in none of 30 Responders versus 6 of 38 NonResponders samples

But this plot likely says that ERBB2 has been mutated only once in both groups

Thank you for any help

[PoisonAlien]

Results in from mafCompare has no ERBB2. Its ERBB4.