Setting gene expression thresholds for trajectory analysis using Monocle
0
3
Entering edit mode
S.Webb6 ▴ 40
@swebb6-19606
Last seen 2.3 years ago

Hello

I am using Monocle to construct pseudotime trajectories on some skin data. Everything has run and it is working fine. Going over my script, I can still see some parameters I have set which I just used from the Monocle tutorial. Looking into them a bit more, I have two main queries:

1.) When I use the detectGenes function at the beginning of my script to filter for genes above a specific threshold value, it is not clear in the documentation where the min_exp values I decide to set are being compared to.

detectGenes(monocleobject, minexpr = 0.1)

I assume it is referring to this table in the Monocle object (monocle_object@assaydata$exprs) but I am unsure.

2.) Before performing a differential gene test across clusters to identify genes which define progression across pseudotime, I use this line from the tutorial to filter for genes present in >x nr cells:

monocleobjectexpressedgenes <- row.names(subset(fData(monocleobject), numcellsexpressed >= 10))

I am unsure how the numcellsexpressed values are computed by Monocle. I know they are taken from the phenodata in the Monocle object but does this just include genes with non-zero values for expression or is it above a threshold? This is not so clear.

Does anyone have any advice on this so I better set these filters?

Thank you

Simone

monocle differential gene expression detectgenes function Tutorial • 372 views
ADD COMMENT
0
Entering edit mode

Hello S.Webb6!

We believe that this post does not fit the main topic of this site.

Monocole isn't a Bioconductor package. If you have questions you should ask somebody in the Trapnell lab.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLY
1
Entering edit mode

Hi James!

Apologies if I have posted incorrectly.

The instructions I used to install Monocle were taken from http://cole-trapnell-lab.github.io/monocle-release/docs/#installing-monocle and included the lines:

source("http://bioconductor.org/biocLite.R")

biocLite()

biocLite("monocle")

library(monocle)

I can also see it listed here in the Bioconductor 3.8 release list: https://www.bioconductor.org/packages/release/bioc/ This is why I thought it was a Bioconductor package - please tell me if I am missing something? I am fairly new to this so maybe I'm making an obvious mistake in understanding what a Bioconductor package is?

Thanks for your help, James

Simone

ADD REPLY
1
Entering edit mode

Sorry, my bad. I have re-opened your post.

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