User: Giuseppe Gallone

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Posts by Giuseppe Gallone

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Answer: A: [DIFFBIND] batch effects and blocking factors
... Hi again Would anyone be willing to help with the issue below? Best wishes Giuseppe On 18/06/14 20:39, Giuseppe Gallone wrote: > Hi > > I have a group of samples for which I'd like to ascertain if > differential binding is detectable based on a "condition" binary > variable (stored ...
written 3.4 years ago by Giuseppe Gallone170
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[DIFFBIND] batch effects and blocking factors
... Hi I have a group of samples for which I'd like to ascertain if differential binding is detectable based on a "condition" binary variable (stored in DBA_CONDITION). However, these samples have been processed in 4 batches (each batch has at least 3 samples). I would like to run a multifactorial an ...
written 3.4 years ago by Giuseppe Gallone170 • updated 3.4 years ago by Gordon Smyth32k
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Comment: C: Package qvalue - can it be installed without TCL-TK support?
... Dear Bernd thanks, I will definitely test it. Best wishes, Giuseppe On 05/23/14 17:32, Bernd Klaus wrote: > Hi Guiseppe, > > If I may shamelessly promote a package from my former group, > > fdrtool (CRAN) > > http://strimmerlab.org/software/fdrtool/ > > essentially uses ...
written 3.5 years ago by Giuseppe Gallone170
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Comment: C: Package qvalue - can it be installed without TCL-TK support?
... Excellent, thanks a lot for your help Best Giuseppe On 05/26/14 04:19, Pengcheng Yang wrote: > As John suggested, the solution is: > > downloaded the package from: > http://www.bioconductor.org/packages/release/bioc/src/contrib/qvalue _1.38.0.tar.gz > > > untar and modify the ...
written 3.5 years ago by Giuseppe Gallone170
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Comment: C: Package qvalue - can it be installed without TCL-TK support?
... John thanks, I will try what you suggested. Best wishes Giuseppe On 05/23/14 15:31, John Blischak wrote: > A short-term solution would be to download the source code and just > directly use the qvalue function. > > wget > http://bioconductor.org/packages/release/bioc/src/contrib/ ...
written 3.5 years ago by Giuseppe Gallone170
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Package qvalue - can it be installed without TCL-TK support?
... Hi I need the qvalue package however I don't need the TCL-TK interface. My R installation was compiled without native TCL-TK support and it is inconvenient for me atm to reinstall/replace etc to add support. As a consequence, as it stands it seems I cannot get qvalue to work on my system. Does a ...
qvalue written 3.5 years ago by Giuseppe Gallone170 • updated 2.7 years ago by Storey, John D.50
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DiffBind - error when setting manual contrast groups
... Hi I'm testing DiffBind using a contrast between two groups containing only one sample each. According to the manual, this is highly discouraged, but possible in principle. I manually set the contrast groups using the construct tamoxifen = dba.contrast(tamoxifen, tamoxifen$masks$Responsive, tamox ...
diffbind written 4.0 years ago by Giuseppe Gallone170
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Comment: C: DEseq for chip-seq data normalisation
... Hi Rory I suppose the analysis I'd like to carry out is conceptually a simpler one than those I was looking at using Diffbind. I'd like to look at the existence-vs-full depletion of peaks at each interval across samples - as opposed to continuous quantitative differences in the peak signal at each ...
written 4.0 years ago by Giuseppe Gallone170
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Comment: C: DEseq for chip-seq data normalisation
... Thanks a lot Rory. Do you think it would then make sense to use the normalised counts in the peaks to build a ratio based on the raw count and then feed this ratio to, say, picard to get a downsampled bam from the original bam? Best Giuseppe On 11/05/13 18:18, Rory Stark wrote: > Hi Guiseppe- & ...
written 4.0 years ago by Giuseppe Gallone170
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Comment: C: DEseq for chip-seq data normalisation
... Hello Sheng I have had biologically interesting results when selecting overlapping peaks between replicates using the IDR. I first call peaks with MACS2 or SPP, using a very loose q-value threshold, and then pass these to the IDR. However, in my experience this works fine between pairs of aligned ...
written 4.0 years ago by Giuseppe Gallone170

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Popular Question 3.4 years ago, created a question with more than 1,000 views. For DEseq for chip-seq data normalisation

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