User: CrazyB

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CrazyB200
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Posts by CrazyB

<prev • 49 results • page 1 of 5 • next >
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Comment: C: references for fold-change cutoff
... Our decision tree is as follows - 1. calculate the fold-change with FDR 2. remove all genes that have FDR >=0.05 3. rank the remaining genes based on fold-changes 4. make an arbitrary cutoff of the fold-change - we set it at a low end (1.2-fold) 5. pool all genes that fulfill the FDR and fold-ch ...
written 7 weeks ago by CrazyB200
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Answer: A: references for fold-change cutoff
... [cancelled by OP - should be a comment not an answer] ...
written 7 weeks ago by CrazyB200
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references for fold-change cutoff
... To my knowledge, there is no consensus cutoff value for the fold-change in transcriptomic data (correct me if this is wrong). However, one reviewer for a submitted manuscript asked that we provide references to support our cutoffs for significance selected. I wonder if there are "good" references ...
cutoff transcriptome fold-change written 7 weeks ago by CrazyB200 • updated 7 weeks ago by Fabio Marroni2.0k
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median probe intensity does not correlate with RNA-seq data - what's the best practice to compare the expression data?
... Looking at RNA-seq data from CCLE (Cancer Cell Line Encyclopedia) from Broad Institute and microarray expression data from NCI-60 cell lines, there is a discrepancy in the "relative" expression level of genes of my interest. Thus I was wondering if there is a "best practice" when we try to pull data ...
microarray rna-seq written 10 weeks ago by CrazyB200
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Comment: C: looking for large human genomes databases
... @ lltommy, @ genomax, my title said that i am looking for human genomes databases. I've now made the changes in the main text to reflect that. ...
written 16 months ago by CrazyB200
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looking for large human genomes databases
... Other than `ExAC` and `GnomAD`, are there any other public human genome databases available that are searchable? `UK10K` seems like a work-in-progress and data are not compiled (thus searchable per dataset but not searchable as a collective group of genome data). A quick google search did not find a ...
genome written 16 months ago by CrazyB200
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how to re-arrange the gene expression heatmap to maximize the visual effect of the result
... I have the mRNA expression data for 4 groups of samples (2-3 samples per group), based on different genetic backgrounds and treatments. While the dendrogram segregates group #1 from the remaining 3 groups at the first branch of the dendrogram, it is not visually clear from the heatmap. Is it possi ...
heatmap written 18 months ago by CrazyB200 • updated 18 months ago by Jean-Karim Heriche17k
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Comment: C: is there a value of ranking genes based on p-value in RNA-seq data
... - @biofalconch - thanks for pointing this out. I completely missed that aspect of the difference between fold-change and p-value. - @CMosychuk - thanks for the link to the Cell paper. Perhaps I did not fully understand the answer in the linked question, but it appeared that the OP in that ...
written 18 months ago by CrazyB200
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is there a value of ranking genes based on p-value in RNA-seq data
... For my RNA-seq project, my collaborator generally provides a list of DEGs and the output is ranked based on p-value, not fold-change. While I understand the significance of p-value in the multiple-testing problems , I have always assumed once a gene passes the p-value cutoff, there is little differe ...
rna-seq written 18 months ago by CrazyB200 • updated 18 months ago by h.mon21k
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interpreting the untransmitted allele in TdT (transmission disequilibrium test)
... Can anyone help shed light on the interpretation/meaning of untransmitted alleles in the TdT test ? For example, in a cohort study, untransmitted SNP1 and transmitted SNP2 are significantly associated with the disease group. As "transmission" of SNP2 is significantly associated with the disease gr ...
tdt written 2.2 years ago by CrazyB200

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