User: lirongrossmann

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Posts by lirongrossmann

<prev • 46 results • page 1 of 5 • next >
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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 20 months ago by lirongrossmann40
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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 21 months ago by lirongrossmann40 • updated 20 months ago by Michael Love25k
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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 21 months ago by lirongrossmann40 • updated 20 months ago by Michael Love25k
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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 21 months ago by lirongrossmann40
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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 21 months ago by lirongrossmann40 • updated 21 months ago by Michael Love25k
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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 21 months ago by lirongrossmann40
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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 21 months ago by lirongrossmann40 • updated 21 months ago by Michael Love25k
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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 ...
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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 21 months ago by lirongrossmann40 • updated 21 months ago by Michael Love25k
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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 22 months ago by lirongrossmann40 • updated 22 months ago by Michael Love25k

Latest awards to lirongrossmann

Popular Question 12 months ago, created a question with more than 1,000 views. For Batch effect removal with Deseq2
Popular Question 12 months ago, created a question with more than 1,000 views. For identifying the samples on plotPCA
Popular Question 12 months ago, created a question with more than 1,000 views. For log fold change threshold in Deseq2 - using lfcthreshold
Popular Question 12 months ago, created a question with more than 1,000 views. For Limma and batch effect

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