User: Vincenzo Capece

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Posts by Vincenzo Capece

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sigGeneSet gage function
... Dear all, I am using gage but I have a problem with the margins of pdf files outputted by sigGeneSet function. In the official gage reference manual there is an option(page 31, 14th April 2013 version): "... other arguments to be passed into the inside gs.heatmap function, which is a wrapper of ...
gage written 5.6 years ago by Vincenzo Capece140
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DEXseq: transcript plot
... Dear all, I have a couple of questions about the plots outputted by dexseq package. 1)In the bottom part of the transcript plot there are several combinations of exons join: Are they all possible combinations of alternative splicing? 2)I am interested to annotate most significance exons, querying PF ...
annotate written 5.7 years ago by Vincenzo Capece140
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Comment: C: DEXseq: several "1" and "NA" in padjust column
... Dear Steve, > all(!is.na(subset(fData(exonCounts), testable)$pvalue)) [1] TRUE > all(is.na(fData(exonCounts)$pvalue) == is.na(fData(exonCounts)$padjust)) [1] TRUE Do you see large fold changes that are getting small pvalues that look like they should be "real"? No I don't Thanks About the ...
written 5.8 years ago by Vincenzo Capece140
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Comment: C: DEXseq: several "1" and "NA" in padjust column
... Thanks a lot Steve. This is the last part of my pipeline(the first part is just the concatenation of strings to build the paths to input files, but they are right): > samples condition replicate 28M_1 28 1 28M_2 28 2 28M_3 28 3 3M_1 3 ...
written 5.8 years ago by Vincenzo Capece140
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DEXseq: several "1" and "NA" in padjust column
... Dear bioconductorers, I am using DEXseq for the splicing analysis. The pipeline works perfectly, but I have some doubts about the output: on 351000 exons I have just 10 padjust significant ones. Googling I found this thread, in which the user developed my same pipeline and in which she has the same ...
dexseq written 5.8 years ago by Vincenzo Capece140 • updated 5.8 years ago by Steve Lianoglou12k
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Comment: C: DEXSeq: building exon count set
... Dear Alejandro, Thanks a lot. I have already used that function and it works perfectly; the problem is to add to this function the transcripts data(with argument "transcripts" in newExonCountSet. For instance, I need to know the start and end position of my exons). With read.HTSeqCount is very easy, ...
written 5.8 years ago by Vincenzo Capece140
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DEXSeq: building exon count set
... Dear all, I am using DEXSeq to make splicing analysis on my data. But I have a problem with the function read.HTSeqCounts: in the countfiles argument, HTSeqCounts get in input a vector with the paths to exon count files, but I have(as in DESeq package) a data.frame like this(computed by my pipeline) ...
deseq dexseq written 5.8 years ago by Vincenzo Capece140 • updated 5.8 years ago by Alejandro Reyes1.6k
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mm10 goseq supported genome
... Dear all, I am trying to analyze RNA seq data with goseq but I have a problem: mm10(the reference genome that I am using for my experiment) is not supported by goseq. The last version supported by goseq is mm9. Can you help me to annotate mm10 RNA seq data with goseq? The version of my goseq is: 1.8 ...
annotate goseq written 5.8 years ago by Vincenzo Capece140 • updated 5.8 years ago by Nadia Davidson270
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Answer: A: DESeq - working with more than 2 conditions
... Thanks a lot Natasha, edgeR is exactly what I was looking for. I am also a statistics beginner and I have an another question ,but I don't know if it's correct or not: To compute BCV in edgeR, why the developers didn't use ANOVA? I think that the MDS in edgeR is s sort of SSB(sum of squares between ...
written 6.1 years ago by Vincenzo Capece140
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DESeq - working with more than 2 conditions
... Dear all, I am a R beginner and I hope you can help me. I have a question about DESeq: DESeq works fine if I have 2 conditions(treated,untreated) Example: treated untreated ENSMUSG00000000001 193 254 ENSMUSG00000000003 0 0 ENSMUSG000000 ...
deseq written 6.2 years ago by Vincenzo Capece140 • updated 6.2 years ago by Wolfgang Huber13k

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