User: romicakerketta

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Posts by romicakerketta

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Comment: C: DiffBind: dba.overlap error
... Thank you for the explanation! ...
written 12 months ago by romicakerketta0
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Answer: A: DiffBind: dba.overlap error
... I guess I figured out the solution to my problem. I had to give a different name when DiffBind reads in the occupancy data and then use a different name when DiffBind reads in counts. Following code worked: DBdata_peak <- dba(sampleSheet=ikras) DBdata_peak #creat count  DBdata <- dba.count(D ...
written 12 months ago by romicakerketta0
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DiffBind: dba.overlap error
... I am using DiffBind for differential occupancy analysis for my Chip-seq data set. The problem I am having is that- as of last week, whenever I ran "dba.overlap" function for my 4 samples (2 samples/condition), I would get 4 overlapping rates (82695,51554,34786,24150). However, When I tried running t ...
diffbind dba.overlap written 12 months ago by romicakerketta0
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Answer: A: biomaRt error in getBM for hsapiens_gene_ensembl
... Hi everyone, try the following code. It is working perfectly fine for me right now. I am working with mouse data and if you are working with other species, just change the name to that of the species. CODE: BiocInstaller::biocLite('grimbough/biomaRt') library(biomaRt) listMarts(mart = NULL, host ...
written 20 months ago by romicakerketta0
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Comment: C: biomaRt error in getBM for hsapiens_gene_ensembl
... I don't know if the Biomart website is updating things right now., but when I run this code again, it is giving me a different error. Fortunately I had saved my variables in a dataframe in R (when I ran the above code), so I am good to go with my analysis. But yeah, I am getting the following error ...
written 20 months ago by romicakerketta0
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Comment: C: biomaRt error in getBM for hsapiens_gene_ensembl
... Hi James, sorry I just joined this website today. I am able to get my data from the biomart website now. Posting the code below for extracting mouse genome data. Same can be repeated for Homo sapiens.  ...
written 20 months ago by romicakerketta0

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