edgeR subsetting DGEList by column/sample
2
0
Entering edit mode
mnaymik ▴ 10
@mnaymik-7522
Last seen 5.2 years ago
United States

I saw this post from a while ago regarding a similar issue: edgeR: Problem with subsetting a DGEList in latest package version

>d$samples[1:6,]

sample                                                   lib.size    norm.factor  type    time

preExercise_TAGGCTGACTTGAG.1      856    1.1020236     B  pre
preExercise_TCCATCCTCGTTAG.1     1033    1.2198739     B  pre
pbmc001_TTGAGGACTTTCAC.1          703    1.2050717     B  pre
pbmc001_AGTCGCCTGCTTAG.1         1230    1.0304974     B  post
pbmc001_TACTACACAGCACT.1         1053    0.9790636     C  post
pbmc001_TAAACAACCCTTAT.1          895    1.1032946     D  pre

...

I am trying to do differential expression of things only of type 'B', with the time frame as the group 'post vs pre'. I though the easiest way would be to just subset d via:

d.B = d[,grep('B',d$samples$type)]

But I get the error:

Error in `$<-.data.frame`(`*tmp*`, "group", value = integer(0)) : 
  replacement has 0 rows, data has 226

Is there a proper way of doing differential expression on just a subset of the DGEList? 

I got around this by employing the method from the post Iinked:

B=grep('B',d$samples$type)
test=DGEList(d$counts)
test=test[,B]

Then replacing test$samples with its proper subset from d:

test$samples=d$samples[Bcells,]

This just seems sort of hacky...

edger subsetting dgelist • 5.3k views
ADD COMMENT
0
Entering edit mode

Something seems strange.

Can you start a new R session, call library(edgeR) and then come back here to update your question with the contents provided by copy/pasting the output of  sessionInfo()

ADD REPLY
0
Entering edit mode

> library(edgeR)

Loading required package: limma

> sessionInfo()

R version 3.3.1 (2016-06-21)

Platform: x86_64-apple-darwin13.4.0 (64-bit)

Running under: OS X 10.11.5 (El Capitan)

 

locale:

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

 

attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base     

 

other attached packages:

[1] edgeR_3.14.0  limma_3.28.14

ADD REPLY
0
Entering edit mode

Can you post a minimal working example of this behaviour?

ADD REPLY
3
Entering edit mode
@steve-lianoglou-2771
Last seen 5 months ago
United States

Now that you've verified you're running the latest version of edgeR, I've looked a bit more closely at your example and error.

It seems that you have somehow constructed a DGEList (d) with a $samples data.frame that doesn't have a group column -- what were the commands you used to construct d?

In any event, try adding a group column, like so:

d$samples <- transform(y$samples, group=paste(type, time, sep="_"))

Then try subsetting by columns again ...

Also, adding such a group column can be useful in  your downstream analysis since you can now analyze your experiment as a one-way layout:

design <- model.matrix(~ 0 + group, d$samples)

You can then construct contrasts with makeContrasts that are easy-to-interpret arithmetic over the columns of design.

 

ADD COMMENT
0
Entering edit mode

Since I was using the time column as my group I had set the samples$group=NULL. Later I had been setting group = time which if I do before subsetting It works just fine. I did not realize group was that sensitive. Thanks!

ADD REPLY
0
Entering edit mode

Or just

d$samples$group <- paste(type, time, sep=".")

would also do the job.

ADD REPLY
0
Entering edit mode
@gordon-smyth
Last seen 27 minutes ago
WEHI, Melbourne, Australia

A DGEList object needs to satisfy some minimum conditions to be a valid object. If you change a DGEList object so that it no longer satisfies these minimum conditions, then operations such as subsetting can no longer be guaranteed to work.

help("DGEList-class") explains what a DGEList object is assumed to contain. It explains that 'group', 'lib.size' and 'norm.factors' are compulsory columns for the d$samples data.frame, so you cannot remove them.

ADD COMMENT

Login before adding your answer.

Traffic: 327 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