Question: Deseq2 PCA Anlysis
0
gravatar for sherajilir
4 months ago by
sherajilir0
sherajilir0 wrote:

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 • 120 views
ADD COMMENTlink modified 4 months ago by Michael Love24k • written 4 months ago by sherajilir0
Answer: Deseq2 PCA Anlysis
0
gravatar for Michael Love
4 months ago by
Michael Love24k
United States
Michael Love24k wrote:

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 COMMENTlink written 4 months ago by Michael Love24k

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.

ADD REPLYlink written 4 months ago by sherajilir0
1

Maybe you could reach out to the data generators to ask about the samples.

ADD REPLYlink written 4 months ago by Michael Love24k
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