EBSeq users

Hi Ning, I am sorry to violate this post. I am wondering if you could spare few minutes to answer my

I have a question about isoform DE analysis when using EBseq From the output of RSEM, I calculated

Hi there, I've been looking through EBSeq's documentation and I couldn't really figure

Hi, I have dataset with timepoints each of three replicates: CondVector <- rep(paste("t"

Hi Christopher, Were you able to address this issue? I have similar concern. There is a contrasting

Hello everyone, I am using rsem output (expected gene counts) to dissect some DE genes in EBSeq. I

Hello, I am new to bioinformatics and am interested in differential expression of lncRNAs. These RNAs

Hi, I get following message and error when I run the EBSeqHMMTest: Conditions are ordered as: d0 d1

Hi, I read in a manual, we need an additional iterations for updateRD parameter in EBSeqHMM function.

Hi Jan, I met the same subscript out of bounds error. Have you solved this problem? Thanks, Xin 在

Hi all, I'm a Ph.D. in bioinformatics at Florida State University. I'm now working on some

Hi EBSeq Users group! I am new to these types of data analysis and have been learning through trial

Hi, I am using EBseqHMM to identify genes following upregulated/downregulated trend across nine time

Hi Pankaj, EBSeq fits a negative binomial distribution on the raw counts. After normalization, your

Hi all, Disclaimer: this is a long post, but I think it is well worth reading and answering to for

Hey, this must be basics but I'm unsure how to implement 2 x 2 setup (two factors, both of which

I have a basic question about the differential expression analyses. When is it appropriate to use

Dear all, I am trying to identify differentially expressed genes using EBSeq . But after running the

Hi, I am using a RSEM count matrix with 20531 rows of genes and 94 samples.This the output of str()

Hi Diana, I encounter the same problem. Did you find the problem finally? Thanks. On Monday, May 23,

Dear EBSeq community, I am using EBSeq on RSEM output in a context of differentially expressed genes

Dear all, I am trying to run EBSeq on a RSEM count matrix containing 2 conditions with 3 replicates

Hello, I am performing many DEG analyses lately, testing with both EBSeq & DESeq2, and EBseq

Ning, Using the above example, is it correct to use Condition 1 as patient and Condition 2 as

Hi Dr. Leng, Thank you for the reply. I was able to run the EBMultiTest for multiple comparison using

Hi I have an experiment in 5 time points without replicates with around 50 000 transcripts. I filter

Hi Guys, Just wandering whether you find out the reasons? I just got a similar strange plots, looks

Hi, Would you mind to send me your data for further debug? Thanks Ning On Mon, Apr 4, 2016 at 2:37 PM

Thank you! > On 22 Mar 2016, at 09:13, Ning Leng <leng...@gmail.com> wrote: > > Yes

Hello, I had the same question as you and Dr Leng told me that she thought that it might be possible.

Hi Shaomin, Seems to me that there are large variabilities within condition (eg outliers and perhaps