User: jennyl.smith12

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Posts by jennyl.smith12

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Subread FeatureCounts for Exon level quantification: Length estimate for Exons as low as 1 base-pair
... Hello,  I am working on quantifying RNASeq data at the exon level, which is intended for use in the DEXSeq package. I followed the documentation provided in the DEXSeq tutorial (http://bioconductor.org/packages/release/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.pdf, page 23), as well as the commands on ...
rnaseq dexseq featurecounts subread written 16 months ago by jennyl.smith120 • updated 16 months ago by Gordon Smyth39k
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Comment: C: Error in DESeq2 Unmix() function: L-BFGS-B needs finite values of 'fn'
... Hi Michael,    Thank you for your response. I examined the correlation of the variance stabilized transformed counts and we do have very correlated pure samples.  The minimum correlation found was still 0.95.  I tried to run the algorithm again using those two pure samples (cor = 0.95), and  I was ...
written 17 months ago by jennyl.smith120
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Error in DESeq2 Unmix() function: L-BFGS-B needs finite values of 'fn'
... Hello,  I wanted to use the unmix() function from DESeq2 to investigate the mixing proportions of normal and tumor from bulk tumor RNAseq.  I was hoping to compare the results from using this function with A) normalized counts from the median ratio method and B) Transcripts per million (TPM). Firs ...
rnaseq deseq2 deconvolution written 17 months ago by jennyl.smith120 • updated 17 months ago by Michael Love26k

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