User: Vanilla

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Vanilla0
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Posts by Vanilla

<prev • 11 results • page 1 of 2 • next >
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Comment: C: DESeq2 design with multiple factors
... Got it. Thanks! ...
written 9 weeks ago by Vanilla0
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Comment: C: DESeq2 design with multiple factors
... Thanks, Michael! That's really great. For the listValues, if I understand correctly, I should put c(1/4, -1/3) for averaging if my contrasts=list(c("1_pos", "2_pos", "3_pos", "4_pos"), c("1_neg", "2_neg", "3_neg")) right? ...
written 9 weeks ago by Vanilla0
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DESeq2 design with multiple factors
... Hi everyone, I have a few samples with the following coldata:   samples    condition    library    time    pos_neg 1 A_1_pos    A_1_pos    A    1    pos 2 A_1_neg    A_1_neg    A    1    neg 3 A_2_pos    A_2_pos    A    2    pos 4 A_2_neg    A_2_neg    A    2    neg 5 A_3_pos    A_3_pos    A  ...
rnaseq deseq2 multiple factor design written 9 weeks ago by Vanilla0 • updated 9 weeks ago by Michael Love20k
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Answer: A: Error with MEDIPS.createSet in queryHits
... Hi all, Thanks for all your help and I finally solved my problems. I tried to solve in two ways: 1. In case it runs over RAM I performed MEDIPS.createSet() chromosome by chromosome. It worked smoothly. However, when calling differentially methylated regions with MEDIPS.meth(), I got the error for ...
written 3.1 years ago by Vanilla0
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Comment: C: Error with MEDIPS.createSet in queryHits
... Hi Herve, Thanks so much for the detailed solutions for my problem. I tried file.exists(paths) and it gave an TRUE. Unfortunately I don't have the right to remove it so I wrote to the admin to update it. Would let you know when it's fixed. :) Best, Vanilla ...
written 3.1 years ago by Vanilla0
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Comment: C: Error with MEDIPS.createSet in queryHits
... Hi Herve, It seems doesn't work... :( I followed your codes and got the following: > R.version.string [1] "R version 3.2.2 (2015-08-14)" > remove.packages("BiocInstaller") Removing package from ‘/nfs/home/package/software/R/lib’ (as ‘lib’ is unspecified) > source("http://bioconductor.org ...
written 3.1 years ago by Vanilla0
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Comment: C: Error with MEDIPS.createSet in queryHits
... Hi Herve, Thanks for pointing out this problem. Actually I'm also concerned about the version issues as I have marked them as bold in my question. The problem is I failed updating BioC3.2 with the following code: source("http://bioconductor.org/biocLite.R") biocLite("BiocUpgrade") As it returned ...
written 3.1 years ago by Vanilla0
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Comment: C: Error with MEDIPS.createSet in queryHits
... Thanks Lukas! I will try out your advice, analyze each chunk of chromosomes and concatenate resulting tables.  -- Best, Vanilla ...
written 3.1 years ago by Vanilla0
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Comment: C: Error with MEDIPS.createSet in queryHits
... Thanks Martin! Would you share some suggestions on chunk-based processing then? -- Best, Vanilla ...
written 3.1 years ago by Vanilla0
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Comment: C: Error with MEDIPS.createSet in queryHits
... Dear Lukas, Thanks very much for your reply. I used 120gb memory to run MEDIPS and actually this is the maximum memory available to me.  Also thanks for your suggestions. However, this is not a merged BAM file. But if memory is the problem caused the error, could I creatSet chromosome by chromosom ...
written 3.1 years ago by Vanilla0

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