User: lirongrossmann

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Posts by lirongrossmann

<prev • 37 results • page 2 of 4 • next >
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Quantile normalization and Deseq2
...  Hi all, I am using variance stabilizing transformation on my rna seq count data with Deseq2. Do I need to use quantile normalize the samples or does variance stabilizing transformation function take care of it?   ...
deseq2 quantile normalization written 22 days ago by lirongrossmann0 • updated 22 days ago by Michael Love14k
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comparing strand-specific counts to unstranded counts
... Hi All, I am trying to compare the level of gene expression between strand specific samples and unstranded samples of rna seq for a set of selected genes.  I ran into a post in biostar : https://www.biostars.org/p/73205/ I wanted to confirm with "Deseq2 experts" here - is this the best way to co ...
rnaseq deseq2 strand written 24 days ago by lirongrossmann0
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identifying the samples on plotPCA
... Hi everyone, I am using deseq2 to find DEG between two groups. I transformed the data using the variance stabilizing transformation and plotted PCA.  I want to label the samples on the PCA plot, is there a way to do it? Here is my code: dds <-DESeqDataSetFromMatrix(countData = ep,colData = cp ...
deseq2 pca plotpca written 28 days ago by lirongrossmann0 • updated 27 days ago by Michael Love14k
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Comment: C: expression matrix with varianceStabilizingTransformation
...  Thanks Dear Wolfgang, One clarification please: if I want to use the genes I got for my Deseq2 to build a machine learning model using a training and validation set, would you use the counts (using the counts data you recommend) or the transformed version of of the data (using the variance stabili ...
written 29 days ago by lirongrossmann0 • updated 29 days ago by Michael Love14k
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Comment: C: expression matrix with varianceStabilizingTransformation
... Thank you !   ...
written 4 weeks ago by lirongrossmann0
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expression matrix with varianceStabilizingTransformation
... Hey all, I have an rna-seq expression matrix and I used Deseq2 to compare gene expression between two groups of in my dataset. I then wanted to to sort the genes I got from Deseq2 according to their levels of expression, and I used  the varianceStabilizingTransformation (vsd) to get the normalized ...
rnaseq deseq2 variancestabilizingtransformation written 4 weeks ago by lirongrossmann0 • updated 29 days ago by Michael Love14k
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Comment: C: differential splicing events and covariates
... Thanks!  I guess I cannot use diffSplice on my matrix with PSI values, correct? ...
written 5 weeks ago by lirongrossmann0
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differential splicing events and covariates
... Hi everyone, I have a file containing psi values for samples and I wanted to compare the differential splicing between two groups of my datasets, adjusting for covariates. Can I just give the dataset of the splicing events to limma? Is there a statistic method especially designed for that kind of d ...
limma rna-seq alternative splicing written 5 weeks ago by lirongrossmann0 • updated 5 weeks ago by Gordon Smyth32k
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Comment: C: Different PCA plots using rlog and vsd on the same data set
... Thanks!  I will try it.  ...
written 7 weeks ago by lirongrossmann0
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Comment: C: RangedSummarizedExperiment in Deseq2 and DESeqDataSetFromMatrix
... exp.... sorry for the typo ...
written 7 weeks ago by lirongrossmann0

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