User: alejandro.colaneri

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Posts by alejandro.colaneri

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Answer: A: Removing genes with very low counts in all samples before run DESeq
... Hi Michael Tx. for the answer. I'm not sure to be able to understand the fundamentals of the statistics supporting filtering in DESeq 2 at this time. I'm a user of this tool more than an expert statistician. However, what about the simple step of removing genes with very low count before run: dds & ...
written 4.7 years ago by alejandro.colaneri20
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Removing genes with very low counts in all samples before run DESeq
... I'm running DESeq to compare two genotypes responding to a treatment. I turn that was not able to see interactions, at least after apply Benj-Hoch for multiple testing correction. I'm thinking in remove genes that are too lowly expressed with the hope that will increase my power. Now my question is, ...
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Comment: C: Error when counting reads in genes with summarizeOverlaps (Genomic-Aligments pac
... Actually when I built the list of path to my files I did not care about that. But the answer is YES, all the bam files in my bam file list have the same name, the original accepted_hits.bam name provided by tophat. Do you think this could be the source of the problem? ...
written 4.7 years ago by alejandro.colaneri20
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Error when counting reads in genes with summarizeOverlaps (Genomic-Aligments package)
... Hello, I'm following the RNA-seq workflow for differential gene expression white paper by Michael Love Simon Anders and Wolfgang Huber.http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=10&ved=0CFcQFjAJ&url=http%3A%2F%2Fwww.bioconductor.org%2Fhelp%2Fcourse-mater ...
rnaseq deseq2 genomicalignments summarizeoverlaps tophat written 4.7 years ago by alejandro.colaneri20 • updated 4.7 years ago by Dan Tenenbaum8.2k

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Popular Question 4.7 years ago, created a question with more than 1,000 views. For Removing genes with very low counts in all samples before run DESeq

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