User: Paolo Kunderfranco

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350
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2 years, 3 months ago
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7 years, 7 months ago
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Posts by Paolo Kunderfranco

<prev • 33 results • page 1 of 4 • next >
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Comment: C: edgeR two conditions two diet treatment
... Dear Aaron, I formatted the table as requested, now it should be much more readable. I read in the user-guide but I find it difficult to create this multi-factor analysis, Best Paolo   ...
written 2.3 years ago by Paolo Kunderfranco350
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edgeR 4 conditions
... Dear All, I am new to multifactor analysis with edgeR, I have the following 12 samples (4 conditions and 3 replictaes) sample type diet sample1 wt no sample2 wt no sample3 wt no sample4 ko no sample5 ko n ...
edger written 2.3 years ago by Paolo Kunderfranco350
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ChIPpeakAnno
... Hi, We used R package ChIPpeakAnno to annotate some ChIP Seq coordinates with respect to the TSS with the script pasted below the message. I was wondering what are exactly the meaning of the features in the pie-chart. To be more exaustly I would like to know what does feature refers to. •  up ...
annotate chippeakanno written 5.5 years ago by Paolo Kunderfranco350 • updated 5.5 years ago by Julie Zhu4.0k
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lumi - limma contrast design
... Dear All, Could you please help me to design a contrast for Differential Analysis? .... constrast.matrix <- makeContrasts ( --------, levels=design) ... I have 4 groups. A - normal B - cancer C - normal + drug D - cancer + drug I would like to find genes modulated in D versus C. These genes ...
cancer written 5.5 years ago by Paolo Kunderfranco350 • updated 5.5 years ago by Axel Klenk940
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EximiR - Limma - miRCURY LNA - Exiqon
... Dear All, I a new in this kind of analyisis. I have to analyze some old data obtained with the technology: miRCURY LNA™ from Exiqon. I use routinely limma and lumi package to anlayze Illumina BeadChip microarray but is the first attempt to analyze data obtained form this platform. I used ExiMiR ...
mirna microarray cancer limma lumi eximir written 5.8 years ago by Paolo Kunderfranco350
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Comment: C: MEDIPS
... Hi Lukas, Specie is mouse, 4 samples plus 2 input, and ws=100. The memory fails when I run MEDIPS.meth for differential analysis between two samples and 1 input. I bypassed the error as you suggested running 3 MEDIPS.meth with chromosomes groups Look forward for the new release! Cheers, Paolo ...
written 6.0 years ago by Paolo Kunderfranco350
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MEDIPS
... Dear All, I am facing some problems with MEDIPS package, I Think I'am running out of memory once I run the command MEDIPS.meth ................ Adjusting p.values for multiple testing... Creating results table... Adding differential coverage results... Error: cannot allocate vector of size 207.9 Mb ...
coverage medips written 6.0 years ago by Paolo Kunderfranco350 • updated 6.0 years ago by Lukas Chavez510
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DiffBind - error dba-count
... Dear All, I come back to DiffBind and tried the new version, I am analyzing some 5hmc and mc Seq experiments in a HPC server. I have both biological replicates and two different peak callers, I first extracted consensus peakset for each replicate. I am facing some problems when I call dba.count ...
diffbind written 6.4 years ago by Paolo Kunderfranco350 • updated 6.4 years ago by Rory Stark2.8k
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MEDIPS
... Dear Lucas Chavez, Repeat masking of the reference genome assembly should be considered before aligning my samples? Or I may loose information? Thanks, Paolo 2013/2/19 Lukas Chavez > > Dear Paolo, > > > why in the example refered in the manual there is only one INPUT.SET for & ...
sequencing alignment medips written 6.5 years ago by Paolo Kunderfranco350 • updated 6.5 years ago by Lukas Chavez510
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Answer: A: MEDIPS
... Dear Lucas Chavez I followed MEDUSA protocol to filter out both not properly paired, low quality mapping and non-unique sequences from my alignment files to use MEDIPS fur further analysis of DMR. For example one mC sample started with 100 milions reads. 80 % mapped, 70 % of them properly mapped w ...
written 6.7 years ago by Paolo Kunderfranco350

Latest awards to Paolo Kunderfranco

Popular Question 2.3 years ago, created a question with more than 1,000 views. For DiffBind - error dba-count
Popular Question 2.3 years ago, created a question with more than 1,000 views. For DiffBind - overlap between different peak callers
Popular Question 5.5 years ago, created a question with more than 1,000 views. For DiffBind - overlap between different peak callers
Popular Question 5.5 years ago, created a question with more than 1,000 views. For DiffBind - sample sheet for multiple replicates and peak

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