User: reubenmcgregor88

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Posts by reubenmcgregor88

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Comment: C: Pathway analysis from list of differentially expressed genes with fold change, p
... I have a long list of about 20,000, from an array. Thanks ...
written 5 weeks ago by reubenmcgregor880
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Pathway analysis from list of differentially expressed genes with fold change, pvalues and normalised expression levels in R
... I have been handed a list of genes from an RNAseq experiment and I have no information about how it was generated as it was done a while ago by a company. I have the lis of genes in columns and pvalues/fold change for different comparisons. I also have the normalised expression values for each gene ...
rnaseq limma R pathway analysis written 5 weeks ago by reubenmcgregor880 • updated 5 weeks ago by Lluís R300
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Comment: C: MA plot DiffBind in ggplot2
... Thanks Rory, Related question, in the dba.report() output, what are the column headers named after the conditions (i.e. Conc_condition1, Conc_condition2). I assume these are what is used in the dba.plotMA the bXY=TRUE and are (as you explained above) log2 transformed values, but form where are thes ...
written 3 months ago by reubenmcgregor880
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MA plot DiffBind in ggplot2
... Hi again, sorry lots of questions at the moment, I would like to replicate the following function from diffBind > dba.plotMA(tamoxifen, bXY=TRUE) ​ However I don't know how to retrieve this data, in Deseq2 I believe it would be the baseMean column. Or is the "Conc" column output by "dab.repor ...
chipseq diffbind R ggplot2 written 3 months ago by reubenmcgregor880 • updated 12 weeks ago by Rory Stark2.2k
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DiffBind broad and narrow peak identification
... Hi,  I have histone, broad-peak data, however some of the peaks are actually rather narrow. So what I can see happening is that the broader peaks are being nicely identified as differentially expressed by diffbind, but the narrow peaks which seem highly up-regulated (with big fold changes) are not ...
chipseq diffbind R written 3 months ago by reubenmcgregor880 • updated 12 weeks ago by Rory Stark2.2k
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Comment: C: DiffBind consensus peak help
... Ok I have an update, when I switched around my sample sheet (I did this purely as I wanted to have the vitd samples as the positive fold change values) to have the vitd samples at the top, the peak in question is now in the  output of > samples_counts.DB <- dba.report(samples_counts, th=0.1, ...
written 3 months ago by reubenmcgregor880
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Comment: C: DiffBind consensus peak help
... Thanks for this, I learned a bit about the dab.report, Here is my sample sheet: SampleID Tissue Factor Condition Treatment Replicate bamReads ControlID bamControl Peaks PeakCaller                         ...
written 3 months ago by reubenmcgregor880
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Comment: C: DiffBind consensus peak help
... Thanks Rory, I have emailed it now ...
written 3 months ago by reubenmcgregor880
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Comment: C: DiffBind consensus peak help
... Hi Gord, Have added to original post, Sorry I will remember this in the future. Seems it is version 2.4.8? -Reuben ...
written 3 months ago by reubenmcgregor880
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DiffBind consensus peak help
...   Hi, I am trying to carry out some differential peak analysis on histone modification data (H3K27Ac data).  I run into problems where one peak in particular is not being called as differentially expressed, where clearly in the data is should be. In order to try and find out where the problem is ...
chipseq diffbind R written 3 months ago by reubenmcgregor880 • updated 3 months ago by Rory Stark2.2k

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