Question

Deseq2 PCA Anlysis

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sherajilir • 0

@sherajilir-18567

Last seen 4.6 years ago

Hello everyone.

I am doing differential expression analysis for a TCGA data set. When i checked PCA separation, i got something like this, a matter i have seen in GSEA as well. Two tumor samples are not separated from the normal.

https://drive.google.com/file/d/1UZh-FQdCw9biCv9AzlfCLAzxLV008cSi/view?usp=sharing

Do you think i should remove these two tumor samples completely?

Thanks in advance.

deseq2 pca • 1.2k views

ADD COMMENT • link updated 5.8 years ago by Michael Love 43k • written 5.8 years ago by sherajilir • 0

score 0 · Answer 1 · 2019-03-21

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Michael Love 43k

@mikelove

Last seen 2 days ago

United States

This isn't a DESeq2 question per say.

I wouldn't remove the samples but I would instead try to use some other program to estimate the purity of those samples.

ADD COMMENT • link 5.8 years ago Michael Love 43k

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Thanks Michael,

I cannot do that since i cannot process the raw files due to lack of computational power. I am relying on raw counts from TCGA extracted by TCGABiolinks.