correlation analysis
1
0
Entering edit mode
6 weeks ago
rheab1230 ▴ 30

Hello everyone, I have two datasets. One is normalised_counts.txt which is the results of deseq2 analysis and the other is a predixcan file which have counts for each gene for all the chromosomes. I have to do Pearson correlation to figure out how many genes in our sample is present in the normalised_counts file. But the problem is that the normalised_Count file is created from rna-seq of bam files for only british ancestry whereas our predixcan file is run on vcf file for all the ancestry. So my doubt is if I do the correlation analysis won't it affect my results since in one file i have only one ancestry and in another I have all.

correlation vcf genes. • 304 views
ADD COMMENT
1
Entering edit mode
5 weeks ago

I have to do Pearson correlation to figure out how many genes in our sample is present in the normalised_counts file.

Taking this statement in its literal sense —and ignoring anything to do with ancestry—, you do not need to do a correlation analysis in order to determine this. Instead, you just need simple filtering criteria with base R functions, like which(), match(), merge(), et cetera

ADD COMMENT
0
Entering edit mode

yes. i was able to do this. i used %in% function to extract those samples. Thank you.

ADD REPLY
0
Entering edit mode

Very good / Muito bem

ADD REPLY

Login before adding your answer.

Traffic: 2384 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