User: correlationmatrix

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Posts by correlationmatrix

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Comment: C: Should p-values resulting from the experimental validation of genes selected by
... Ok. In this case the validation experiment only considers 5 genes. So strictly speaking, multiple hypotheses are being tested and additionally the experiment uses another setup, so the null hypothesis would be different. I guess then it would be appropriate to correct for multiple testing. ...
written 4 months ago by correlationmatrix20
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Comment: C: Should p-values resulting from the experimental validation of genes selected by
... A concrete example that may clarify what I mean: That the original screen was an shRNA dropout screen, where the changes in the abundances of shRNAs that mediate knockdown of various genes were assessed between two time points. According to this screen, shRNAs targeting Gene 1,2,3,4 and 5 were sign ...
written 4 months ago by correlationmatrix20
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Should p-values resulting from the experimental validation of genes selected by FDR also be FDR-corrected?
... Let's say you perform a large number of statistical tests based on some high-throughput screen. Since you are afraid that some of the resulting p-values could have arisen by chance, you perform FDR-correction and only proceed with those whose p-values are < 5% likely to be wrong. Subsequent stati ...
fdr p-values multiple testing validation written 4 months ago by correlationmatrix20 • updated 4 months ago by Nicolas Rosewick5.5k
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Criteria for excluding genes from Fisher tests (presence of mutation vs sample group). Minimum number of samples mutated?
... I would like to test a number of different genes as to whether a mutation in that gene is significantly associated with a particular group of samples. Thus, for each gene I will perform a Fisher test to compare the number of samples in group A with any mutation in gene 1, vs the number of samples in ...
fisher samples mutation written 7 months ago by correlationmatrix20 • updated 7 months ago by theobroma221.0k
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Comment: C: How to output all variant alleles at a given site, regardless of quality
... You're right, that was the issue! ...
written 10 months ago by correlationmatrix20
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Comment: C: How to output all variant alleles at a given site, regardless of quality
... Works! Although in this case I was only interested in looking up specific regions, but subsetting the BAM file using samtools first solves the problem. However, I got some Java errors when running callvariants.sh: "Invalid maximum heap size: -Xmx101593m. The specified size exceeds the maximum repre ...
written 10 months ago by correlationmatrix20
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How to output all variant alleles at a given site, regardless of quality
... How can one use either samtools mpileup or any other tool to, for a given position, output all alternate alleles regardless of quality? Just "samtools mpileup" (and the parameters I've tried so far) gives <*> for a position for which I observe an alternate base in IGV. (The purpose of doing th ...
variant snp mpileup written 10 months ago by correlationmatrix20 • updated 10 months ago by Brian Bushnell14k
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Issues when scaling the TOM:s for consensus network construction with WGCNA
... Hi! I am attempting to perform a consensus co-expression network analysis with WGCNA based on two datasets (same experiment). Everything seems alright until I reach the step where one should scale the topological overlap matrix of dataset 2 to be comparable to the one derived from dataset 1. Speci ...
wgcna written 10 months ago by correlationmatrix20

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