Quality checking by biological replicates

Question

[zizigolu]

HI

I have two data setes, in which some samples are from the same patients (library preparation has not been performed at the same time), and some samples are not from the same patients but we have 4 cell lines definitely from the sample patients in two plates (higlighted in yellow)

This is the samples and controls are in yellow

![enter image description here][1]

You imagine I have two plates like this

How I know if the these plates are replicable? Can I just simply look at the correlation of gene expression of these 4 cell lines between two plates?

Thank you for any thoughts

Answer 1

[Kevin Blighe]

Hello again,

You don't have many data-points but, yes, just correlation and / or try car::scatterplotMatrix()

Kevin

[zizigolu]

Thank you so much @Kevin Blighe

Sorry in the main plate layout, for some samples (Wells) I have duplicates

How do I deal with the duplicates here? Do I average them first? Do I pick the first replicate? Do I use both replicates? (If I do the last one won’t it bias the results towards the samples that are in replicate?)​

These questions all turn around replicated samples

Please look at this sheet, some samples are single, some duplicated and some triple (in highlighted column)

![enter image description here][1]

Please, you may share your thoughts here?

Thank you once more

[Kevin Blighe]

Good evening, are these technical or biological replicates (duplicates)? If they are technical, then you can obtain the average (mean) value.

[zizigolu]

They're replicates. So we took from the same pooled RNA 

So it wouldnt be tumour heterogeneity, but technical variations

Does this mean I should average them

Thank you

[Kevin Blighe]

I think yes, i.e., these are technical replicates and, therefore, you can average them.