User: sxv

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sxv0
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Posts by sxv

<prev • 5 results • page 1 of 1 • next >
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Comment: C: Filtering extraneous samples affects DESeq results. What is going on?
... Sure is. And now I am remembering that I read it before. Thanks again for your patience and light speed. ...
written 3 months ago by sxv0
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Filtering extraneous samples affects DESeq results. What is going on?
... This has probably been addressed before, but I am wondering why I am seeing different results for contrasting the same groups of samples. Let's say I have 30 samples, sequenced in two batches, with 10 each having diagnosis: normal, tumor, invasive. The objective is to obtain a list of genes that ar ...
deseq deseq2 written 3 months ago by sxv0 • updated 3 months ago by Michael Love26k
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Comment: C: DESeq2 formula to include batch AND patient, and condition ?
... There are between 1 and 4 Tumor samples per patient, and sometimes (but not always) a Normal sample. ...
written 4 months ago by sxv0
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DESeq2 formula to include batch AND patient, and condition ?
... Hi, I have 26 samples from 12 patients sequenced in two batches. 6 of these are "normal" samples while the other 20 are tumors. What I have done before is simply compare the tumors against the normals, and include the batch variable as follows: design.file$batch <- as.factor(design.file$batch) ...
deseq2 written 4 months ago by sxv0 • updated 4 months ago by Michael Love26k
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DESeq2 contrast with list no longer works: all elements of the contrast as a list of length 2 should be elements of 'resultsNames(object)'
... Hi, I am encountering an error which I cannot solve when attempting a contrast that references a list. "dx" is a column in my design file and each sample row has a value of "dx1", "dx2", or "dx3" in this column. "batch" is a column with three possible values "group1", "group2", "group3". Now I w ...
deseq2 written 22 months ago by sxv0 • updated 22 months ago by Michael Love26k

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