User: pkachroo

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pkachroo10
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Posts by pkachroo

<prev • 15 results • page 1 of 2 • next >
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Comment: C: Discrepancy in extracting contrasts
... Thanks for your quick response. You are right, despite resultsNames(dds) not showing all three contrasts, I am able to extract the results.      ...
written 13 months ago by pkachroo10
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Discrepancy in extracting contrasts
... Hi,   I am trying to account for batch effect in the DESeq2 design as follows: ddsFull<-DESeqDataSetFromMatrix(countData=countsTable, colData=colData, design=~batch+group) My covariate of interest is "group" and has three levels 1A, 1B, 2A. I have 2 batches - A and B that need to be accounted ...
deseq2 contrast batch effect resultsnames written 13 months ago by pkachroo10 • updated 13 months ago by Michael Love20k
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Comment: C: Differences in PCA plot - rld versus vsd normalized data (DESeq2)
... Thanks, once again. I realized that I had not added the batch variable, but I had already posted my response by then (Oops). Okay, so I used the following command and replotted PCA:  assay(vsd)<-removeBatchEffect(assay(vsd), vsd$batch)  The PCA plots looks like this now: I see less defined c ...
written 15 months ago by pkachroo10
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Comment: C: Differences in PCA plot - rld versus vsd normalized data (DESeq2)
... Hi Micheal, Sorry, I reran the design and didn't get the error anymore. Must be a mistake on my end. I used the following design:  ddsFull<-DESeqDataSetFromMatrix(countData=countsTable, colData=colData, design=~batch+status+group) vsd_b <- varianceStabilizingTransformation(dds, blind=FALSE) ...
written 15 months ago by pkachroo10
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Comment: A: Differences in PCA plot - rld versus vsd normalized data (DESeq2)
... Thanks for your help Micheal. Based on the comments on Bioconductor DESeq2 threads, I understood that I can remove batch effects by simply accounting for it in the design. I tried the following command: ddsFull<-DESeqDataSetFromMatrix(countData=countsTable, colData=colData, design=~ batch + grou ...
written 15 months ago by pkachroo10
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Differences in PCA plot - rld versus vsd normalized data (DESeq2)
... Hi all, I generated PCA plots for my RNASeq data (3 biological replicates per sample) using rld and vsd normalized count data (images below).  I then removed data for three samples that appeared like outliers on the PCA plots (marked in red circle) and also I know that those three samples have m ...
deseq2 batch effect pca written 16 months ago by pkachroo10
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Comment: C: PCA plot in DESeq2
... Thanks Micheal. I complete agree with your reasoning. However, I have 30 samples in triplicates and visualizing the relationship between samples become difficult due to multiple data points. I intend to make both PCA plots, with individual replicates (to see spread within samples) and with average o ...
written 22 months ago by pkachroo10
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PCA plot in DESeq2
... Hi, For RNASeq analysis, I am generating a PCA plot for various strains with three biological replicates each. When I make the PCA plot , I get a symbol on the plot for every replicate. For a large dataset, I was wondering if there is a way to have a single symbol (average of three biological repli ...
deseq2 pca plot written 22 months ago by pkachroo10 • updated 22 months ago by Michael Love20k
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Comment: C: Comparing two RNASeq protocols using DESeq2
... Thanks Micheal. I made a PCA plot of expression data from 5 strains done using both protocols and although each protocol retains the relationship between strains, expression data generated using two protocol appears distinct (PC1). I wonder what is contributing to this ? The spread of the counts, us ...
written 22 months ago by pkachroo10
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Comment: C: Comparing two RNASeq protocols using DESeq2
... After re-running with DESeq(dds, betaPrior=FALSE) and results(dds, cooksCutoff=FALSE), I looked at the DE genes and this time both protocol called more DE genes, genes for protocol2 with adjpavlue as NA (e.g. gene 14) were now differentially expressed, but gene1, as you thought, did not pass the thr ...
written 22 months ago by pkachroo10

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Popular Question 17 months ago, created a question with more than 1,000 views. For PCA plot in DESeq2

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