User: francesca3

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francesca320
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Posts by francesca3

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Sicer - Peak calling-Filter called peaks based on scores
... Hi, after having called peaks with Sicer2 using the same parameters for each sample but calling them individually (one command line for each sample), is it correct to filter peaks based on a threshold put on the SCORES given by SICER? Or I should normalize values in some way before doing it? Thank ...
chip-seq peakcalling sicer written 29 days ago by francesca320
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Comment: C: Extract RPKM values from Diffbind
... Thank you Rory. I have another question. When I retrieve these RPKM values I obtain very low numbers (ranging from around 0.5 to 2). Which values should I expect for trusted regions? If I retrieve TMM values (DBA_SCORE_TMM_MINUS_FULL) these values range from around 10 to 200. Usually I was counting ...
written 4 weeks ago by francesca320
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Extract RPKM values from Diffbind
... Hi everyone, does anyone know if there is a way to extrapolate rpkm values from Diffbind?? Thanks Francesca ...
rpkm diffbind chip-seq written 4 weeks ago by francesca320 • updated 4 weeks ago by Rory Stark730
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Missing a row name in Heatmap.2
... Hi, I use heatmap.2 (from ggplots) to produce heatmaps. Sometimes I notice that I miss a row name... It could be the first row, but other times it is in the middle. This is the code heatmap.2(unitomatrice, scale="row", col=palette, density.info="none", colRow = FALSE, trace="none", distfun = f ...
R ggplots written 3 months ago by francesca320 • updated 3 months ago by RamRS28k
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CSAW- functions not present
... Hi everyone, I'm trying to run csaw on Windows10 x64 system using R 3.6.6 and R 3.6.1 and I'm not able to find some functions, such as filterWindowsGlobal, mergeResults. Besides, when I try to use the filterWindows function putting both the counts and the background, it says that the background and ...
csaw chipseq csaw; chip-seq written 4 months ago by francesca320 • updated 4 months ago by ATpoint36k
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Comment: C: Diffbind- results different every time I run it
... Can you specify which kind of details do you need? This is the format of my table ` SampleID,Factor,Replicate,Condition,bamReads,Peaks, PeakCaller, PeakFormat ` Number of replicates: SIRT630=6 WT30=5 In one group (SIRT630) the factor (SIRT6) is overexpressed, in the other not. The chip was immun ...
written 4 months ago by francesca320
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Diffbind- results different every time I run it
... Hi everyone. I'm new at Diffbind. I'm trying to analyze my data but I noticed that if I try to run the same analysis more times on the same data (restarting from the first line of code), the results change. How is it possible? I clean the environment everytime because initially I thought that it cou ...
software error diffbind written 4 months ago by francesca320 • updated 3 months ago by Michael Dondrup47k
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Diffbind-edgeR or Deseq2
... Hi everyone, I'm using the DIffbind package and I'm noticing that there is a huge difference in the number of diff binding sites found by edgeR and Deseq2. I'm using the default options in dba.analize, just putting the object that I want to analyze and setting method=DBA_ALL_METHODS. For example i ...
chip-seq written 4 months ago by francesca320 • updated 4 months ago by ATpoint36k
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Answer: C: ChipQC doesn't run
... I found the problem. There is a bug when the package is used from PC. It needs to launch this command register(SerialParam()) before launching the CHIPQC command Thanks ...
written 5 months ago by francesca320
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ChipQC doesn't run
... Hi everyone, I'm having troubles with ChipQC. I load the samplesheet and I try to run the ChIPQC function but several errors appears: chipObj<-ChIPQC(samples, annotation="mm9") Bam file has 22 contigs Error: BiocParallel errors element index: 1, 2, 3 first error: do ...
chip-seq written 5 months ago by francesca320 • updated 5 months ago by RamRS28k

Latest awards to francesca3

Scholar 5 months ago, created an answer that has been accepted. For C: ChipQC doesn't run

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