Question

deseq2 estimating size factors

1

Entering edit mode

gv ▴ 40

@gv-6516

Last seen 3.2 years ago

United States

Hi Everyone,

I am trying to run DESeq2 package in R. After running the package I have few questions. I will start with this.

baseMean : It is defines as average of the normalized count values, dividing by size factors, taken over all samples in the DESeqDataSet

After this step of the analysis,

ddsMat <- DESeqDataSetFromMatrix(count, colData, design=~condition

I ran

ddsMat <- DESeq(ddsMat)

In the above calculation I see estimating size factors

I want to know how I can get estimating size factors. What I want to do is to confirm the value of baseMean generated in the table for a particular gene.

How can I do this?

Thanks

Regards

Varun

r deseq2 • 3.5k views

ADD COMMENT • link updated 9.6 years ago by Michael Love 43k • written 9.6 years ago by gv ▴ 40

score 3 · Answer 1 · 2016-04-15

3

Entering edit mode

Michael Love 43k

@mikelove

Last seen 1 day ago

United States

There are a couple of approaches to finding information about a Bioconductor package. You can type:

vignette("DESeq2")

if you search the vignette for "size factors", one of the hits is in a section called "Access to all calculated values".

You can also browse all the DESeq2 manual pages by typing:

help(package="DESeq2", help_type="html")

If you search this page you will find some topics on size factors, including how to access the estimated size factors.

ADD COMMENT • link 9.6 years ago Michael Love 43k

0

Entering edit mode

Hi Michael

Thanks for your reply. I found what i was looking for. Also how can i know which functions can be applied on CLASS DESeqDataSet? For example estimateSizefactors(dds), what else??

Thanks

ADD REPLY • link 9.6 years ago gv ▴ 40

1

Entering edit mode

The complete list of methods is:

methods(class=class(dds))

But this includes *everything* that works on this object, including all the methods from the classes DESeqDataSet inherits, and you probably just want the package specific functions.

I wrote some messy code which gets this:

intersect(sapply(strsplit(as.character(methods(class="DESeqDataSet")), ","), `[`, 1), ls("package:DESeq2"))

This is an intersection between the character string of the methods names...

as.character(methods(class="DESeqDataSet")

...(after removing the class name parts of the signature) and the functions in the DESeq2 package...

ls("package:DESeq2")

Maybe there is a better way.

ADD REPLY • link 9.6 years ago Michael Love 43k

1

Entering edit mode

Martin pointed me to:

showMethods(classes="DESeqDataSet", where=getNamespace("DESeq2"))

And you can get a short list with this messy code:

sub("Function: (.*) \\(package .*\\)","\\1",grep("Function",showMethods(classes="DESeqDataSet", where=getNamespace("DESeq2"), printTo=FALSE), value=TRUE))

ADD REPLY • link 9.6 years ago Michael Love 43k