Question: How to compare the expression of a gene for some samples compared to the rest of the samples?
gravatar for BPors
10 months ago by
BPors30 wrote:

I am trying to see the distribution of expressions of certain genes for certain patients, and want to compare them for the rest of the patients. For example, for 4 genes and 50 patients, some have values and some has no information for gene expression (empty):

IDs         Patient1  Patient2 ... Patient 50
Gene1       value1     value2        value3                  
Gene2       value4     value5        value6
Gene3                  value7
Gene4       value8

How to plot the distribution of expression of Gene1 for Patient1 and Patient 2 ( value1 and value2 ), versus the other 48 Patients ( other 48 values belonging to rest of the patients) ?

rna-seq expression gene • 351 views
ADD COMMENTlink modified 10 months ago • written 10 months ago by BPors30

In the example that you give, you're just comparing the expression of a gene in 2 patients versus 48 patients? That won't produce reliable statistics due to the fact that it's imbalanced and that one group has very low numbers (n=2).

Can you elaborate further on your experiment? For example, do you just want to perform differential expression analysis between 2 groups of patients and are just asking how to do that?

In which format, currently, is your data?; how was the data produced?


ADD REPLYlink written 10 months ago by Kevin Blighe35k
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