Human genes correlation to Bacterial genes

Question

[saamar.rajput]

I have read counts for RNAseq data for human and bacteria with three replicates each. I have transformed the absolute read counts to Z-scores and now I want to do correlation analysis between the Z-scores of the human genes and the bacterial genes.

My data looks like this

 head(Human)

                          R1           R2           R3
  ENSG00000000003.12 -0.005805397 -0.004682964 -0.004462534
  ENSG00000000005.5  -0.010862624 -0.008231991 -0.009366348

 head(Bacteria)

              R1           R2           R3
  BP0001  0.4561311  0.317043968  0.345781788
  BP0002 -0.1443091 -0.158057523 -0.073588398
  BP0003  0.2459770 -0.004348217 -0.013678371

I want to correlate every human gene with every bacterial gene. I used the following command

ct = cor.test(Human, Bacteria, method = "pearson")

I have two questions, Firstly, I am not sure if this would work as I want or not. Secondly before that I have an error, since the two dataframes are not equal.

Error in cor.test.default(Human, Bacteria, method = "pearson") : 
   'x' and 'y' must have the same length

Can somebody tell me how to use the cor.test function with unequal dataframes.

[GenoMax]

Curious as to what kind of an experiment is this?

[saamar.rajput]

I am trying to correlate every single human gene with every single bacterial gene by pearson correlation using the the read counts of the genes.

[Kevin Blighe]

When you correlate, you have to have the same number observations in the vectors that you are correlating. You cannot just randomly correlate any data-matrices.

The only way that you can do this is by correlating each row of Human with each row of Bacteria, but then you only have 3 observations going into each correlation test and the statistics will be virtually meaningless and not credible.

Please try to come up with a better way of comparing human and bacterial genes by doing a literature search on the topic. Your analysis would be better if you had more observations.

[GenoMax]

Can you confirm biological logic behind this comparison? Something that is happening in bacteria correlates to human gene expression (or vice-versa)?

[saamar.rajput]

To identify bacterial and human genes with similar expression kinetics

[arta]

You can combine the two data frame using human.bacteria <- rbind(Human, Bacteria) than do correlation analysis.