User: Prasad Siddavatam

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Posts by Prasad Siddavatam

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Comment: C: deseq2 - PCA plot
... Thank you very much Bernd, for your detailed explanation.  ...
written 4.7 years ago by Prasad Siddavatam150
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Comment: C: deseq2 - PCA plot
... Thank you very much Michael, In this scenario, I don't have the option of re-sequencing the samples but trying to including the existing sample in the analysis and explain the reasons for the inclusion.  Luckily, my heatmap shows that all the control samples are clustered in the hierarchical cluste ...
written 4.7 years ago by Prasad Siddavatam150
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Comment: C: deseq2 - PCA plot
... The abnormal point I am talking about is located at the left bottom (purple square)   ...
written 4.7 years ago by Prasad Siddavatam150
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Comment: C: deseq2 - PCA plot
... Hi Michael, Thank you very much for the help. here is the link for the plot http://i.imgur.com/q6fTtKp.png   ...
written 4.7 years ago by Prasad Siddavatam150
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deseq2 - ignore a replicate
... Hi Michael, I am having hard time with one of the replicates in a three replicate experiment. This is a control sample. But the other replicates look good on PCA plot and also on pairwise scatter plot comparison. Can I ignore this one replicate and perform the deseq2 analysis. I understand that the ...
deseq2 written 4.7 years ago by Prasad Siddavatam150 • updated 4.7 years ago by Michael Love25k
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Comment: C: deseq2 - many differentially expressed genes
... I am not talking about the PCA plot, with respect to the small counts(nc RNAs), but the number of DE genes.  ...
written 4.7 years ago by Prasad Siddavatam150
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Comment: C: deseq2 - many differentially expressed genes
... Hi Michael,  Thank you very much.  Another potential problem could be coming from the data itself because the list of genes in the data are ~45k and many of these include microRNAs and other noncoding RNAs. Since the data is coming from mRNA, having these genes (even with zero counts) in the matri ...
written 4.7 years ago by Prasad Siddavatam150
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deseq2 - PCA plot
... Hi Michael, I am analyzing a dataset (treatment vs. control) each with three replicates. In the PCA plot one of the replicate samples (control) is positioned away from the other two replicates but the treatment samples are nicely clustered. How do you deal this scenario? Is there any required modif ...
deseq2 written 4.7 years ago by Prasad Siddavatam150 • updated 4.7 years ago by Bernd Klaus560
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deseq2 - many differentially expressed genes
... Hi Michael, I am following up on our previous discussion, I ran DESeq2 with minReplicatesForReplace=Inf and cooksCutoff=FALSE and it actually increased the number of DE genes.  Here is the sample code dds <- DESeqDataSetFromMatrix(countData = countsMatrix, colData = colData, ...
deseq2 written 4.7 years ago by Prasad Siddavatam150 • updated 4.7 years ago by Steve Lianoglou12k
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Answer: A: deseq2 - many differentially expressed genes
... Also I set cooksCutoff to FALSE and increased the number of differential genes.    Here is the sample code dds <- DESeqDataSetFromMatrix(countData = countsMatrix, colData = colData, design = ~ type); dds <- DESeq(dds); Gres <- results(dds, contrast=c("type","ABCD_DIF","ABCD_UND"), cooks ...
written 4.7 years ago by Prasad Siddavatam150

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Popular Question 4.7 years ago, created a question with more than 1,000 views. For deseq2 - PCA plot

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