User: lirongrossmann

Reputation:
40
Status:
New User
Location:
Last seen:
10 months ago
Joined:
1 year, 10 months ago
Email:
l*************@yahoo.com

Posts by lirongrossmann

<prev • 46 results • page 1 of 5 • next >
0
votes
1
answer
282
views
1
answer
Handling outliers in Deseq2
... Hello everyone, I am using Deseq2 to perform differential gene expression between 2 groups (each 14 samples) using the following code: ep<-read.table("counts.txt",header = TRUE, row.names = 1)  cp<-read.csv("Annotation.csv") dds <-DESeqDataSetFromMatrix(countData = ep,colData = cp,desig ...
deseq2 outliers logfoldchange written 18 months ago by lirongrossmann40
5
votes
1
answer
1.1k
views
1
answer
log fold change threshold in Deseq2 - using lfcthreshold
... Hi Everyone,  I am running a rna seq differential gene expression experiment with the following code: dds <-DESeqDataSetFromMatrix(countData = ep,colData = cp,design =~Age+Gender+Response) dds <- DESeq(dds) res <- results(dds,contrast=c("Response","Yes","No")) Looking at the results I g ...
deseq2 lfcthreshold written 18 months ago by lirongrossmann40 • updated 18 months ago by Michael Love24k
0
votes
1
answer
553
views
1
answer
Base mean count threshold
... Hi all, I have an rna seq dataset for which I used Deseq2 to find differentially expressed genes between two groups. I got many genes (in the thousands) with adjp <0.1, but the base mean varies from 0.5 to 5000 depending on the gene. Is there a common threshold people use to filter based on the ...
deseq2 base written 18 months ago by lirongrossmann40 • updated 18 months ago by Michael Love24k
0
votes
1
answer
1.0k
views
1
answers
Comment: C: Batch effect removal with Deseq2
... Thanks! Can I use the output for classification purposes as well or would you recommend a different strategies for accounting for confounders? ...
written 19 months ago by lirongrossmann40
1
vote
1
answer
1.0k
views
1
answer
Batch effect removal with Deseq2
... Hello everyone, I was wondering if there is a way to remove batch effect from an expression matrix (raw counts) for downstream analysis (like pca, clustering, machine learning) using the Deseq2 package.  I know I can do it using limma with removeBatchEffect, but wasn’t sure if there’s a similar fu ...
limma deseq2 removebatcheffect() batch effect written 19 months ago by lirongrossmann40 • updated 19 months ago by Michael Love24k
0
votes
2
answers
496
views
2
answers
Answer: A: an unexplained phenomenon using variance stabilizing transformation for downstre
... Thank you very much for the clarification!! My biggest issue is which values to use in order to train the model? Should I use the normalized values or should I used the transformed values (which if I understand correctly are also normalized). I used "mat" to train my model based on the "Response cl ...
written 19 months ago by lirongrossmann40
0
votes
1
answer
807
views
1
answer
choosing the normalization method (rlog, variance stabilizing transformation)
... Hi everyone, I was hoping to get an answer on an issue I have been struggling for a while.  I have a raw count data from RNA-seq experiment and want to develop a model for separating two group of samples. I used Deseq2 to select my top genes and trained and test the model on the dataset using vari ...
deseq2 variancestabilizingtransformation rlog transformation written 19 months ago by lirongrossmann40 • updated 19 months ago by Michael Love24k
1
vote
2
answers
496
views
2
answers
an unexplained phenomenon using variance stabilizing transformation for downstream analysis
... Hi Everyone, I am using variance stabilizing transformation (vsd from now on) for normalization in order to perform downstream analysis on a raw count expression matrix. To be specific, I have two groups (say group A and group B) that I want to separate based on the expression levels of certain gen ...
1
vote
1
answer
300
views
1
answer
NA adjp with extremely low p value
... Hi all, I ran Deseq2 and got several genes with NA adjp with a very low p value. How can I find the associated adjp with that gene? Thanks  ...
deseq2 adjusted pvalue written 19 months ago by lirongrossmann40 • updated 19 months ago by Michael Love24k
0
votes
1
answer
306
views
1
answer
Distribution of transformed data using VST
... Hi Everybody, I would like to use variance stabilizing transformation on rna seq raw count samples to build a machine learning model in order to predict two classes. I wanted to use linear discriminant analysis, but was not sure if I can assume that the transformed data are distributed normally.  ...
deseq2 variancestabilizingtransformation written 20 months ago by lirongrossmann40 • updated 20 months ago by Michael Love24k

Latest awards to lirongrossmann

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 171 users visited in the last hour