RNA-seq batch effect remove

Question

[9521ljh]

i have TCGA RNA seq dataset(sample number: 11) and my own dataset(sample number : 11)

i want to compare TCGA and my own dataset expression level.

However, i find that my own datasets have lot of read counts(output from RSEM) overall.

Thus, i feel need to do remove batch effect within TCGA dataset and within my own dataset. Then remove batch effect between TCGA dataset and my own dataset.

then i found the edgR tools. and do remove batch effect.

Before remove batch effect. before remove batch effect

"1" indicates TCGA data.

"2" indicates my own data.

After remove batch effect. after removing batch effect code by edgeR

at this point, i want to confirm the batch effect is really remove or not.

[Ram]

Please see How to add images to a Biostars post to add your images properly. You need the direct link to the image, not the link to the webpage that has the image embedded (which is what you have used here)

[lessismore]

Go for a PCA analysis and check if you still have clustering based on technical variability.