How to find genes causing the high variance of one replicate in the PCA
1
1
Entering edit mode
NMostajo ▴ 10
@nmostajo-10900
Last seen 5.3 years ago
Germany

Hello, 

I have checked the PCA from my sRNAseq data and there is one replicate which goes over 67% away from all my samples (1/18).

I know that the PCA plots the genes with the top variance, and this sample seems to not have crazy values in all the genes (checked random), and with PCA of different biotype class genes (miRNAs and snoRNAs)

Pvars <- rowVars(assay(rld))

topVarGenes <- head(order(rowVars(assay(rld)), decreasing = TRUE),35)

with this I found the genes with the highest variance, but I do not seem to identify the genes that are causing the "crazy" behavior of this sample.

I do not want to throw away the sample because I only have 3 replicates, and the behavior seems to be caused by a few genes. Also the cooks plot shows it as the other samples.

Any suggestion on how to find the genes that are causing the extreme behavior in one replicate?

Thank you!

 

pca variance deseq2 gene_id • 762 views
ADD COMMENT
2
Entering edit mode
@mikelove
Last seen 23 hours ago
United States

Here's one quick approach to look for genes where a sample has extreme counts. Use vst(), rlog() or normTransform() and then extract the transformed values with assay():

mat <- assay(vsd)
zscores <- t(scale(t(mat)))
hist(zscores[ ,idx ]) # where idx is the number of the sample
gene.idx <- which(zscores[,idx] > x) # where x is a large value
plotCounts(dds, gene.idx[1])
ADD COMMENT
0
Entering edit mode

Thanks! I got my gene IDs

ADD REPLY

Login before adding your answer.

Traffic: 369 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6