User: bekah

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bekah0
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Posts by bekah

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Comment: C: MethylKit read in issue
... However the second script is still not working - is this likely to be an issue with the output format from bismark? Error in `[.data.frame`(data, , 6) : undefined columns selected In addition: Warning message: In fread(filepath, ...) :   Starting data input on line 2 and discarding line 1 because it ...
written 9 weeks ago by bekah0
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Comment: C: MethylKit read in issue
... please see above - already solved, but cheers :) ...
written 9 weeks ago by bekah0
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Comment: C: MethylKit read in issue
... solved - no need for the extra script file.list=list("CpG_90.txt", "CpG_96.txt") # read the files to a methylRawList object: myobj myobj=methRead(file.list,                 sample.id=list("IN190","CON96"),                assembly="onilo11",                treatment=c(1,0),                context="C ...
written 9 weeks ago by bekah0
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MethylKit read in issue
... Afternoon! I am having trouble with methylkit read in - I have the methylcall output context files from bismark which I am trying to read into MethylKit. However I am getting the same error after trying to read in as a raw methyl object  Error in fread(filepath, ...) :    Input is either empty or f ...
rrbs methykit written 9 weeks ago by bekah0 • updated 9 weeks ago by Mike Smith2.8k
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Comment: C: Pre-filtering genes counts vs normalised counts DESeq2
... Oh sorry I think I found it counts(dss, normalized =TRUE) ​just in case anyone else was looking for this also ...
written 10 weeks ago by bekah0
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Pre-filtering genes counts vs normalised counts DESeq2
... Hi, ​I am working on RNA-seq data and looking to prefilter my data - I was using the sum of the read counts >100, but then read that I could use the normalised read counts instead? Is this a better filter, as it is based on data normalised across all samples? I am struggling to be able to view t ...
deseq2 pre-filtering written 10 weeks ago by bekah0 • updated 10 weeks ago by Michael Love18k
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Comment: A: LRT results DESeq2
... Ah cheers! So this can be used to identify if the DEG I have found when looking at the four individual experimental groups (infected L, infected H, control L, control H) can be attributed to the difference in temperature or difference in status?   ...
written 10 weeks ago by bekah0
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LRT results DESeq2
... Hi, ​I am running analysis on RNA Seq data using DESeq2, I have two "treatments" for each sample each with two levels status: sham or infected temperature: high or low. ​I have run the LRT to look at whether I am make sure I have not made any assumptions based on experimental design on whether ge ...
deseq2 job written 10 weeks ago by bekah0
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Comment: C: Estimating group-specific dispersion in DESeq2
... ​This was the pca created from logtransformed data using blind = FALSE to make sure biological variation from treatment was not smoothed out excessively. Colours are the experimental treatment groups (i.e. 5 replicates per treatment). I think that the dispersal is too varied and independent pairwi ...
written 15 months ago by bekah0
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Comment: C: IHW Package for R 3.2.5
... cheers - is all sorted, managed to call the latest R version and run as admin to get the packages needed to install  ...
written 15 months ago by bekah0

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Popular Question 14 months ago, created a question with more than 1,000 views. For DESeq2 not installing

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