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 16 months ago by lirongrossmann20
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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 17 months ago by lirongrossmann20 • updated 16 months ago by Michael Love23k
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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 17 months ago by lirongrossmann20 • updated 16 months ago by Michael Love23k
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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 17 months ago by lirongrossmann20
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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 17 months ago by lirongrossmann20 • updated 17 months ago by Michael Love23k
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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 17 months ago by lirongrossmann20
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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 17 months ago by lirongrossmann20 • updated 17 months ago by Michael Love23k
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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 18 months ago by lirongrossmann20 • updated 17 months ago by Michael Love23k
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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 18 months ago by lirongrossmann20 • updated 18 months ago by Michael Love23k

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