Question

filter factor DGEList

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dojo89 • 0

@dojo89-24417

Last seen 3.5 years ago

Hello together,

I am new in the R universe and working with RNAseq data from three different cell lines. For analysis I am using edgeR. Now, I have two batches of data. I plotted them all together in a MDS plot. If I compare the controls in each batch per cell line I found a lot of differential expressed genes for one cell lines. To get a better idea of what is going on I would like to create a MDS plot exclusively with this cell line while ignoring the other two. For that I was wondering if I could to some kind of filtering of the DGEList-object. My sample names are factors in "y_keep[["samples"]][["group"]]" But because it is a factor all my trials to sort them were unsuccessful....

Could you help me with this? Thanks :)

edger • 658 views

ADD COMMENT • link updated 3.5 years ago by Gordon Smyth 50k • written 3.5 years ago by dojo89 • 0

Gordon Smyth · Answer 1 · 2020-10-21

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Gordon Smyth 50k

@gordon-smyth

Last seen 28 minutes ago

WEHI, Melbourne, Australia

Just subset the DGEList by column, for example something like

plotMDS( y[,CellLine==1] )

ADD COMMENT • link 3.5 years ago Gordon Smyth 50k

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Thanks for the fast response :) I have already tried it and received this error massage:

> plotMDS(y_keep[,samples=="HCC4006"])
Fehler in h(simpleError(msg, call)) : 
  Fehler bei der Auswertung des Argumentes 'j' bei der Methodenauswahl für Funktion '[': Objekt 'samples' nicht gefunden

Any further idea?

Thanks a lot!

ADD REPLY • link updated 3.5 years ago by Gordon Smyth 50k • written 3.5 years ago by dojo89 • 0

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Well, you don't have an object called samples in your session so naturally you get an error. You haven't shown us what is in your data object but I am guessing that you need:

j <- y_keep$samples$group=="HCC4006"
plotMDS(y_keep[,j])

You will need to get some familiarity with base R in order to use edgeR comfortably. We assume that people are familiar enough with base R to be able to use the "$" operator. So y_keep$samples is a data.frame contained in y_keep and group is a factor contained in y_keep$samples.

I suggest you do a bit of exploring, for example:

names(y_keep)
names(y_keep$samples)
head(y_keep$samples)
table(y_keep$samples$group)

ADD REPLY • link 3.5 years ago Gordon Smyth 50k