Question: (Closed) featureCounts to DESeq2: Unable to form object and divide it unequally
0
gravatar for swarajgaikwad15
4 months ago by
Tezpur University, Assam, India
swarajgaikwad150 wrote:

I am following one blog RNA seq analysis - FeatureCounts and DESeq2 workflow, but I am unable to understand for what purpose does this [,5] is used

colnames(counts)[6:11]=str_split_fixed(colnames(counts)[6:11],"\\.",6)[,5]

another thing here I want to divide my data unequally i.e., in 14 and 7 then how I can modify this following command

samples=cbind(colnames(counts)[6:11],str_split_fixed(colnames(counts)[6:11],"_",3)[,2])

Here they have divided their sample into 2 equal groups each of 3 samples

I didn't find any suggestion or solution related to the str_split_fixed function. Any help or suggestion in this regard is deeply appreciated.

ADD COMMENTlink modified 11 weeks ago by Biostar ♦♦ 20 • written 4 months ago by swarajgaikwad150

The protocol given in this manual Count matrix input, seems confusing therefore I am following the blog.

ADD REPLYlink written 4 months ago by swarajgaikwad150

You should simply go step by step and check the output of each step. Then you will learn.

ADD REPLYlink written 11 weeks ago by Kevin Blighe41k

Hello swarajgaikwad15!

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

There is no real problem

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 REPLYlink written 11 weeks ago by Kevin Blighe41k

I can see why the blog post potentially added extra work for other people on Biostars to respond to. However, this seems relevant to Biostar discussions, and I think other people should be able to post comments (although I can see why the person writing the blog and the DESeq2 tutorial should probably be the primary sources of information).

ADD REPLYlink written 11 weeks ago by Charles Warden6.6k
1

Precisely, Charles, the composer of the blog should address this. By putting material on the WWW, one must take responsibility. swarajgaikwad15, please contact the composer of the blog.

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by Kevin Blighe41k
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