User: ssabri

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ssabri10
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Posts by ssabri

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Comment: C: Using IRanges to find gene TSS that overlap a window
... It appears this does the same as the above code? How would I restrict the overlap such that the overlap counts only if the TSS is included within the window?  ...
written 3 months ago by ssabri10
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Using IRanges to find gene TSS that overlap a window
... I only want to find genes that have start positions located within a defined range window. If there are no overlaps I want to return NAs for the column fields that describe the overlap. However if there is an overlap with a gene start, then I want to return the gene start and end locations as well a ...
iranges granges R written 3 months ago by ssabri10 • updated 3 months ago by Haibo.Liu0
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Building a pseudo-network based on correlations
... I have clustered a few points and have computed the mean of each cluster as a landmark point for that cluster. I have then computed a correlation matrix among all landmark points to see which are most similar. Now I'd like to *connect* each landmark points to its two most similar neighbors. Since th ...
R ggplot2 written 12 months ago by ssabri10 • updated 12 months ago by Matthias Z.20
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Comment: C: How to properly normalize a single-cell sparse matrix?
... So, I've sampled two cells at random and made a few MA plots as you've suggested and have linked to the results below.  y = raw_data[, c("RandCellA","RandCellB")] plot(x=rowMeans(y), y=y[,1]-y[,2]) # (plot A, linked below) plot(x=rowMeans(log2(y)), y=log2(y[,1])-log2(y[,2])) # (plot B, linked belo ...
written 14 months ago by ssabri10
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Comment: C: How to properly normalize a single-cell sparse matrix?
... Hmm I'll check out the paper! Looks interesting but we do not work with ERCC spike-in controls. Can your method still be applicable?   ...
written 14 months ago by ssabri10
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How to properly normalize a single-cell sparse matrix?
... I am having issues trying to properly normalize single-cell Drop-seq data. My Drop-seq data consists of single-cells (columns) with very sparse transcript gene counts (rows). A summary of the number of non-zero genes (rows) per cell (column) is posted below:  > summary(colSums(data != 0)) Mi ...
normalization single-cell dropseq sparse written 14 months ago by ssabri10 • updated 14 months ago by Aaron Lun17k
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Comment: C: Deseq2 error estimating size factors -- zeros in count matrix
... Excellent! Thank you so much for the clarification. This has answered my question. ...
written 22 months ago by ssabri10
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Comment: C: Deseq2 error estimating size factors -- zeros in count matrix
... For this particular analysis I simply intend to do some data visualizations. I don't believe there would be any need to do differential expression which is why I only want to transform my data (via VST).  I must have overlooked the `type="iterate"` option! Thank you for bringing this to my attentio ...
written 22 months ago by ssabri10
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Deseq2 error estimating size factors -- zeros in count matrix
... I am posting in regards to an error I've experience when running Deseq2's estimateSizeFactors. The specific error is posted below:  > dds = DESeqDataSetFromMatrix(countData=filteredDGE, colData=design, design=~condition) converting counts to integer mode > dds = estimateSizeFactors(dds ...
deseq2 estimatesizefactors written 22 months ago by ssabri10 • updated 22 months ago by Michael Love14k

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Popular Question 22 months ago, created a question with more than 1,000 views. For Deseq2 error estimating size factors -- zeros in count matrix

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