Question: Statistical test to compare expression change in a subgroup of genes versus all genes?
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gravatar for biostart
3.8 years ago by
biostart350
Germany
biostart350 wrote:

Dear statisticians:

Suppose I have two cell conditions, and the processed RNA-seq data for both of them, giving expression log2 fold changes.

I want to test a hypothesis that a subgroup of genes is upregulated statistically stronger than all the genes. So, I am creating a column with log2 fold changes of all genes whose changes are statistically significant (say, 10k genes), and a second column with log2 fold changes of the genes belonging to my subgroup of interest, whose changes are statistically significant (say, 1k genes). Then I calculate two-sample t test for these two groups of genes. And I get a P value which is quite low.

Please comment, whether I am doing it right?

Thanks

PS. Someone suggested that I should be using Mann-Whitney Test instead of the two-sample t test. Could statisticians please comment on this?

rna-seq • 1.5k views
ADD COMMENTlink modified 3.8 years ago by h.mon30k • written 3.8 years ago by biostart350

Did you use the same background to find significant genes in both sets, are the two sets independent?

ADD REPLYlink written 3.8 years ago by H.Hasani920

yes, the significance was determined once for all the genes using the standard workflow, I am not changing it when splitting genes into subsets

ADD REPLYlink written 3.8 years ago by biostart350

I'm not sure in this case if it is correct to use the t-test (see Independent t-test using SPSS Statistics). If you are interested in addressing the strength of a statistical signal (the fold changes) you could use volcano plot.

hth

ADD REPLYlink written 3.8 years ago by H.Hasani920

I was not using independent t-test, I was using two sample t-test

ADD REPLYlink written 3.8 years ago by biostart350
0
gravatar for h.mon
3.8 years ago by
h.mon30k
Brazil
h.mon30k wrote:

It sounds like you want to perform a Gene Set Enrichment Analysis, the R/Bioconductor gage has all the framework you need, see its page here and this manual on how to prepare custom gene sets.

ADD COMMENTlink written 3.8 years ago by h.mon30k

Thank you, but I would prefer to not use any blackbox solutions, I want to understand what I am doing

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by biostart350
2

The documentation and publication belonging to those tools are quite clear about what's going on, it's not a blackbox solution.

There is a difference between understanding what you are doing and reinventing the wheel.

ADD REPLYlink written 3.8 years ago by WouterDeCoster44k
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