User: kerrypop

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kerrypop0
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Posts by kerrypop

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P-value distribution acceptable for qvalue
... In the qvalue vignette, it states data with a U-shaped p-value histogram is a red flag. If distribution resembles either of the following, is it appropriate to use this package? Thank you. ...
qvalue pvalue histogram written 5 months ago by kerrypop0 • updated 5 months ago by Laurent Gatto840
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Comment: C: ComBat to remove batch effects from RNA Seq data
... Pawel, Sorry for the delay in my response. I was traveling the past 2 weeks. I greatly appreciate your feedback and am eager to try the different methods. I previously used the following code to remove lowly expressed genes and wanted to check if it was an appropriate method.  getVar <- apply( ...
written 12 months ago by kerrypop0
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ComBat to remove batch effects from RNA Seq data
... Hi,  I want to use ComBat to remove batch effects from RNA Seq data. Have 2 batches, both consisting of disease and healthy samples, processed at different times. Can I use FPKM normalized data as input for ComBat or do I have to perform some normalization using the raw counts? Thank you  ...
rnaseq combat written 13 months ago by kerrypop0 • updated 13 months ago by polemiraza40

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