Question: DE analysis of genes with different number of samples in Tumor and control group
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gravatar for hAjmal
4 months ago by
hAjmal30
hAjmal30 wrote:

Hi, I am usng TCGA biolinks to do DE analysis of genes in the breast cancer TCGA data. The number of samples in normal and tumor groups are different. Is is possible to do DE analysis with different number of samples in each group? Please guide.

ADD COMMENTlink modified 12 weeks ago by Biostar ♦♦ 20 • written 4 months ago by hAjmal30

Hi hAjmal, how many is "different"? Please give some numbers.

ADD REPLYlink written 4 months ago by ATpoint23k

112 normal and 1100 tumor samples

ADD REPLYlink written 4 months ago by hAjmal30
1

I would guess (not being a statistician) that the dispersion estimates at these high sample numbers should be sufficiently stable regardless of the uneven group sizes. You can of course run several analysis with subsets of the tumor group and see if the results are stable when subsampling.

ADD REPLYlink modified 4 months ago • written 4 months ago by ATpoint23k
1

If these are a randomly selected set of normal and tumour samples then it's fine. The issue I suspect you may have here, is that the normal may actually be non-tumour tissue from a tumour-proximal site in a subset of the cancer patients; if so, you will need to match the patient-derived samples.

ADD REPLYlink written 4 months ago by russhh4.7k

As your normal is too less compared to case, you may get biiased result..... Increase the number of Normal or lessen the number of case. Equal set is always preffered.

ADD REPLYlink modified 4 months ago • written 4 months ago by Ranan Jyoti Sarma40

The number of samples is not a concern here, the batch effect is. You best option is to match tumor and healthy, another option is to add the batch as a covariate, let's hope the tumor and healthy are not grouped separately.

ADD REPLYlink written 12 weeks ago by Asaf6.2k
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