DEXSeq related query

[shikha5]

Hi
My name is shikha and currently I am working on RNA seq data analysis. I want to compare two different tissue samples eg: one from kidney tissue and another from liver (not replicates of same sample) in terms of differential exon usage and for this purpose I thought DEXSeq tool is the right option but when I am using the command for creating ExonCountSet objects its showing an error:

Error in strsplit(rownames(dcounts), ":") : non-character argument

I don't know how to proceed with two different samples if possible using this tool.

Any suggestions in this regard are highly appreciable.

Thanks,

Best regards,
Shikha Vashisht.

[dpryan]

1) Can you post the exact code you used that produced the error? It'll be easier for people to figure out the problem then.

2) Do you mean to say that you want to compare 2 individual samples and not 2 groups of samples drawn from different tissues (e.g. 4 kidney samples vs. 4 liver samples)? If so, you're not going to get much useful from any program. Elsewhere on this site, Simon Anders (I think) posted the DEXSeq equivalent of the DESeq "blind" dispersion method, but I wouldn't recommend bothering with that for the aforementioned reasons.

[shikha5]

Thanks for the reply dpryan.
Yes, I am trying to compare two individual samples from two independent tissues.

[shikha5]

This is the code I am using for getting the ExonCountSet Object:

ecs<-read.HTSeqCounts(countfiles=file.path("ERR030894_mapped_reads_dexseq_chr.counts"),("ERR030895_mapped_reads_dexseq_chr.counts"),flattenedfile=("Homo_sapiens_flattened_chr.gff"))

[areyes]

Hi @shikha5,

The error message should me more informative, but the error is coming because you are using only one samples. In order to use DEXSeq, in the most simple of comparing two conditions, you should have at least two replicates for each condition, meaning 4 samples.

Alejandro

[shikha5]

Thanks Dear Alejandro for replying and giving you valuable suggestion.

Okay in that case I should have two replicates of kidney tissue sample and two for the other one and it will compare between the replicates variability of same tissue but not between two individual samples. Am I correct??

[areyes]

Yes, that sounds fine. With four samples, the function "read.HTSeqCounts" should not complain anymore.

[shikha5]

What If I want the comparison between two individual tissues then according to you which program/tool can serve the need at this moment??