What function in edgeR normalize the reads between samples?
1
0
Entering edit mode
冠宇 • 0
@881bb85a
Last seen 14 months ago
Taiwan

Hello everyone:

I am working on the RNA-seq data with edgeR recently. I tried to find which function normalizes the reads between samples and found that the "betweenLaneNormalization" and "calcNormFactors" could be that function.

I read the description of "betweenLaneNormalization". It says, "Between-lane normalization for sequencing depth and possibly other distributional differences between lanes.", but I only input the gene count of samples not including any information about lanes. I don't know "betweenLaneNormalization" normalize for what. Does the term "lane" mean the lane in the sequencing chip?

edgeR • 833 views
ADD COMMENT
0
Entering edit mode
@gordon-smyth
Last seen 4 hours ago
WEHI, Melbourne, Australia

edgeR doesn't need to normalize reads because normalization is handled by models, as explained in the edgeR User's Guide section on "normalization".

betweenLaneNormalization() is not an edgeR function and is not needed for an edgeR analysis.

What analysis are you trying to do and why do you believe you need to normalize reads between samples?

ADD COMMENT
0
Entering edit mode

Sorry, I put this question in the wrong place.

We want to compare the CPM between samples, so we want to normalize the unwanted variance, like different library sizes and miscounting by the outliers.

As far as I know, betweenLaneNormalization() is a function from EDAseq and it can scale the count I think it can deal with the variance from different library sizes.

I still don't understand the function of calcNormFactors. I found that the cpm() output is different before and after the calcNormFactors, but I don't know how it works.

ADD REPLY
0
Entering edit mode

The standard recommended way to obtain CPM or log-CPM values in edgeR is by

y <- calcNormFactors(y)
logCPM <- cpm(y, log=TRUE)

and this will normalize between samples and account for different library sizes. There is no need for any other functions.

Type help("calcNormFactors") to read what calcNormFactors() does.

ADD REPLY
0
Entering edit mode

Thanks for your advice!!

ADD REPLY

Login before adding your answer.

Traffic: 929 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