Question

Deseq2 PCA Anlysis

0

Entering edit mode

sherajilir • 0

@sherajilir-18567

Last seen 4.0 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 • 1.0k views

ADD COMMENT • link updated 5.1 years ago by Michael Love 41k • written 5.1 years ago by sherajilir • 0

score 0 · Answer 1 · 2019-03-21

0

Entering edit mode

Michael Love 41k

@mikelove

Last seen 16 hours 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 5.1 years ago Michael Love 41k

0

Entering edit mode

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.