Question: Comparing RNA expression between different tissue type, but same Cancer.
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gravatar for 9521ljh
5 months ago by
9521ljh20
9521ljh20 wrote:

i have 40 SARCOMA data. and there are many groups of tissue.

if i use RNA expression normalization method, is it okay to compare?

More specific, if i have 12 bone tissue sarcoma and 28 Uterus tissue type.

using these 40 sample, the edgeR results in MDM4 gene is differentially expression in tumor than normal.

i think it is nonsense to compare.

am i right?

rna-seq • 147 views
ADD COMMENTlink modified 5 months ago by i.sudbery8.4k • written 5 months ago by 9521ljh20
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gravatar for i.sudbery
5 months ago by
i.sudbery8.4k
Sheffield, UK
i.sudbery8.4k wrote:

Sarcoma just means a cancer of non-connective tissue. So bone sarcoma and uterine sarcoma are not the same cancer. However.... If you have matched tumour and normal for each sample (that is, you have 12 bone normals and 28 Uterus normals), there is no statistical reason you can't compare both tissue types together. Note however, that as you have 28 uterine and only 12 bone, lots of your results would probably be uterine genes, whose effect sizes had been diluted by the presence of the bone samples.

You could have tissue type as an explanatory variable. You would probably then find genes that are common cancer genes (i.e. likely upregulated in any cancer).

ADD COMMENTlink written 5 months ago by i.sudbery8.4k

Sincerely really thank you!

ADD REPLYlink written 5 months ago by 9521ljh20
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