User: noname

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noname0
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Posts by noname

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Comment: C: DESeq2, outlier correction, Combat, NMF
... Yes, this is bulk RNA-seq. The three batches were done with the same protocol as well As for the values I get, I checked a few genes after the outliers were corrected and the new values seemed reasonable and in line with the other samples. ( I am not sure how to get a list of the 4036 genes DESeq2 f ...
written 2.5 years ago by noname0
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Comment: C: DESeq2, outlier correction, Combat, NMF
... Sadly I have no idea why a single gene in a sample could have such a high count. They seem to be random. I went with DESeq2 for the outlier correction because of the inherent filtering steps, lib correction, as well as the option to specify batch as part of the model. I imagine if I am not able to ...
written 2.5 years ago by noname0
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DESeq2, outlier correction, Combat, NMF
... Hello, I am wondering if you can advice me on my latest project. I have 3 batches of mRNA-seq with 50, 40, 100 samples (same protocol). My end goal is to use NMF to cluster the samples. I noticed that there are ~200 genes with very high expression values (100k+ raw counts) spread between the samp ...
deseq2 combat outliers nmf written 2.5 years ago by noname0 • updated 2.5 years ago by Michael Love26k

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