# Why are my Chi-squared test results different from those in a published table?

I recently read the paper “A novel long non-coding RNA linc-ZNF469-3 promotes lung metastasis through miR-574-5p-ZEB1 axis in triple negative breast cancer”. In this I see Table1 showing correlation of Linc-ZNF469-3 with different features in TNBC and non-TNBC patients. p-values are calculated based on Pearson's Chi-sq test.

For non-TNBC patients: I calculated the p-value with the Chi-sq test just to have a look if everything is right.

Recurrence:

data <- data.frame(x= c(40,62), y=c(56,65))
data
chisq.test(data, correct = F)

Pearson's Chi-squared test

data:  data
X-squared = 1.1269, df = 1, p-value = 0.2884


Brain:

data <- data.frame(x= c(6,99), y=c(6,119))
data
chisq.test(data, correct = F)

Pearson's Chi-squared test

data:  data
X-squared = 0.096461, df = 1, p-value = 0.7561


You can see that the Recurrence p-value doesn't match with what I see in the table. Others, like Brain, Bone, Liver, Lung match with the p-values I calculated.

And for TNBC patients, not a single p-value matches with my calculations. I don't even get Lung and Bone as having significant p-values with my calculations.

I did it for Lung as shown here:

data <- data.frame(x= c(25,143), y=c(9,35))
data
chisq.test(data, correct = F)

Pearson's Chi-squared test

data:  data
X-squared = 0.8044, df = 1, p-value = 0.3698


But in the paper they mentioned:

We found that high linc-ZNF469-3 expression was significantly correlated to lung metastasis in TNBC patients (Table 1).

Can anyone tell me what could be the wrong here? Is it my calculation wrong? or in the paper?

• Ouch. This probably warrants a correction or even retraction. Oct 9 '18 at 11:07
• Exactly. I have another question. Lets say Lung p-value in TNBC patients is significant. High linc-ZNF469-3 has 9 and low linc-ZNF469-3 has 25. How could one tell that high linc-ZNF469-3 expression was significantly correlated to lung metastasis in TNBC patients? Oct 9 '18 at 11:31
• We found that high linc-ZNF469-3 expression was significantly correlated to lung metastasis in TNBC patients (Table 1). This conclusion can not be reached. Mar 22 '20 at 6:47
• We found that high linc-ZNF469-3 expression was ignificantly correlated to lung metastasis in TNBC patients (Table 1). This conclusion can not be reached. Metastasis across tnbc and non-tnbc require a different analysis e.g. t-test. Mar 22 '20 at 6:55