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PCA analysis of RNA-seq data #6

Open annashcherbina opened 7 years ago

annashcherbina commented 7 years ago

rna_pc1_pc2_control_treated rna_pc1_pc3_time rna_pc2_pc3_reps

rna_var_explained

annashcherbina commented 7 years ago

Re-running PCA on rlogTransform(counts) suggests the absence of surrogate variables.

One idea we discussed earlier was removing key drivers of PC1, if PC1 did not correlate to DMSO treatment or timepoint, but it looks like that is not the case -- PC1 splits between DMSO treated and control in the rlogTransform(counts) space:

rlogtransformcounts_varplot rlogtransform_counts_pca

Running PCA on asinh(tpm):

asinh_tpm_varplot asinh_tpm_pca

and with removal of the surrogate variables:

asinh_tpm_minus_sva_varplot asinh_tpm_minus_sva_pca

akundaje commented 7 years ago

That's great. This makes sense to me. Can discuss in person tomorrow briefly.

Anshul

On Apr 27, 2017 5:11 PM, "annashcherbina" notifications@github.com wrote:

Re-running PCA on rlogTransform(counts) suggests the absence of surrogate variables.

One idea we discussed earlier was removing key drivers of PC1, if PC1 did not correlate to DMSO treatment or timepoint, but it looks like that is not the case -- PC1 splits between DMSO treated and control in the rlogTransform(counts) space:

[image: rlogtransformcounts_varplot] https://cloud.githubusercontent.com/assets/5261545/25509161/ca46fa38-2b6b-11e7-804a-67abf7957fc9.png [image: rlogtransform_counts_pca] https://cloud.githubusercontent.com/assets/5261545/25509165/cf3f72ae-2b6b-11e7-9168-fece0110ceb7.png Running PCA on asinh(tpm):

[image: asinh_tpm_varplot] https://cloud.githubusercontent.com/assets/5261545/25509179/e7984aa6-2b6b-11e7-9701-f387492eedfe.png [image: asinh_tpm_pca] https://cloud.githubusercontent.com/assets/5261545/25509180/e9b65e7c-2b6b-11e7-8868-4cbadda6d9ba.png and with removal of the surrogate variables:

[image: asinh_tpm_minus_sva_varplot] https://cloud.githubusercontent.com/assets/5261545/25509266/86a5b1b0-2b6c-11e7-8971-4f7078adbd00.png [image: asinh_tpm_minus_sva_pca] https://cloud.githubusercontent.com/assets/5261545/25509268/89d68378-2b6c-11e7-9558-3c4781cc0b8a.png

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