User: Diana

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Diana10
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7 months, 3 weeks ago
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10 months ago
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Posts by Diana

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Error dataframe in data.frame: replacement has 1 row, data has 65
... Hi all, When running the following code: library(qusage) library(nlme) # upload gene sets gmtfile <- file.path("hallmarkgeneSets.gmt") hallmarkgeneSets = read.gmt("hallmarkgeneSets.gmt") # define log2 matrix eset <- top500logcpm fi ...
qusage weird r error written 8 months ago by Diana10
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Answer: A: Qusage/nlme package for adding random effects in gene set enrichment analysis
... I have found a solution: it is sufficient to provide the column name of the design (so in my case: fixedeffects <- ~SVZstatus instead of fixedeffects <- Design$SVZstatus). Now it works. :) ...
written 8 months ago by Diana10
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Qusage/nlme package for adding random effects in gene set enrichment analysis
... Hi there! I am trying to perform a gene set enrichment analysis with qusage package in order to incorporate one random effect. I am comparing two groups of patients on one contrast (which is basically my only fixed effect in my design) and I have multiple samples per patient (which is my random eff ...
qusage gsea written 8 months ago by Diana10
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Comment: C: Memory issues in summarizeOverlaps funtion
... Really? So simply running se will actually count all reads? That would be great... But how is it possible that tail(assay(se)) gives 9997 as last row and rowRanges(se) gives an object of length 25892? I am sorry for asking these probably basic questions... ...
written 9 months ago by Diana10
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Comment: C: Memory issues in summarizeOverlaps funtion
... Hi, I have still one question about the reduceByYield argument. I have the following code: > csvfile <- file.path("W29-1-1.csv") > sampleTable <- read.csv(csvfile,row.names=1) > sampleTable File 1 W29-1-1-B 2 W29-1-1-F > setwd("C:/Program Files/ ...
written 9 months ago by Diana10 • updated 9 months ago by James W. MacDonald51k
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Comment: C: Memory issues in summarizeOverlaps funtion
... Sorry, currently I am reading in one file. As for the yieldSize argument, I know it exists. I haven't yet tried it, as I assumed it would take a looong time to read the whole file in seperate chunks. I will try it with a yieldSize of 2000000 to start with. ...
written 9 months ago by Diana10
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Comment: C: Memory issues in summarizeOverlaps funtion
... Hi James, Thanks for your answer! Yes, I am reading BAM files. I know the yieldSize argument, but the file itself is about 500 MB, so isn't the memory error a bit strange? What could be an explanation besides low RAM memory (which is not the case)? ...
written 9 months ago by Diana10
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Memory issues in summarizeOverlaps funtion
... Hi all, I get a memory error ('error: cannot allocate vector of size 344.5 Mb') when running summarizeOverlaps in the Genomic alignments package. I have 4 GB RAM (with about 3.8 GB free space) and I use 64 bits R. I also increased the memory.limit size to 3500 and I tried -- vanilla as well. Noth ...
summarizeoverlaps memory written 9 months ago by Diana10 • updated 9 months ago by James W. MacDonald51k
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Splicing large bam file with Rsamtools
... Dear all, I tried to open a bam file with the following script: library(Rsamtools) bam<-scanBam("~/Bamfiles Ivy/W9.1.1.bam") As a result, a memory error occured: Error in value[[3L]](cond) : 'Realloc' could not re-allocate memory (209715200 bytes) file: C:/Users/Dia ...
rsamtools written 9 months ago by Diana10 • updated 9 months ago by Martin Morgan ♦♦ 24k
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RSubread in cygwin
... Hi, I am trying to download the Rsubread package through cygwin, but I can't find Subread in the packages offered in cygwin. Is there any other way to download Rsubread on my windows based computer? Thanks in advance! ...
subread written 10 months ago by Diana10

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