User: fusion.slope
fusion.slope • 200
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Posts by fusion.slope
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... Hello,
does anybody of you has never tried to generate null model of DNA sequences in mouse using the gkmSVM package? It works perfectly for human but for mouse it does not. I am wondering if any of you have never used this package for mice and had the same problem.
The error problem when I u ...
written 6 months ago by
fusion.slope • 200
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... you can select cut-off threshold to work with significant SNP. The cut-off threshold should be selected according to sample size to avoid false positive results. A P.val <= 0.01 is a good start but again, select a cut off for eQTL or GWAS or QTL depends on the number of SNPs that you are testing ...
written 7 months ago by
fusion.slope • 200
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... you have a table that might be the output of a tool that is performing such eQTL or QTL analysis, so please formulate again your question. What do you want to know? ...
written 7 months ago by
fusion.slope • 200
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... make a screenshot of the dataset and I can tell you more. I am not in the condition now to download 63.3 Mb of a file. ...
written 7 months ago by
fusion.slope • 200
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... Yes i can confirm, I also highly recommend Matrix eQTL, it is extremely fast and you can add covariates if any in your experimental design. ...
written 7 months ago by
fusion.slope • 200
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... I have a similar problem:
I have a list of genes differentially expressed in cell B between "control vs Knock Out" experiment. I want to see if there is an overlap (and via hypergeometric test that is not just by chance) between the genes down-regulated in the Knock out cell B with genes that ar ...
written 7 months ago by
fusion.slope • 200
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Comment:
C: Probability of gene list overlap
... are the 2 lists from the same cell type? ...
written 7 months ago by
fusion.slope • 200
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... Hello,
I have to select the background for a hypergeometric test that I have to perform. The problem is as follow:
I have a list of genes differentially expressed in cell B between "control vs Knock Out" experiment. I want to see if there is an overlap (and via hypergeometric test that is not j ...
written 7 months ago by
fusion.slope • 200
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... oh thanks a lot, I have scrolled a bit the file but did not go down enough to see the ENSEMBL gene annotation! much appreciated genomax! ...
written 8 months ago by
fusion.slope • 200
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... thanks a lot, i think alex already answered my question :) but to confirm i should check rsem output to see which gene_id reference they use.. ...
written 8 months ago by
fusion.slope • 200
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