User: inzirio

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inzirio10
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Posts by inzirio

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Answer: A: diffbind change conditions dinamically
... Hi Rory, thanks for replying! I know about the contrasts, but I'd like to dinamically change the labels for each sample in the conditions column. Is there a way to do that on the dba object? It is because I need to do some permutation of the samples in order to do some tests with some fake data. ...
written 4 months ago by inzirio10
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diffbind change conditions dinamically
... Hi, once loaded a dba object, and already computed the counts, is there a way to change only the design conditions column in order to perform the further steps? I just want to shuffle the sample conditions without computing the counts again in order to perform the contrasts. Thanks, inzirio ...
diffbind conditions edit written 4 months ago by inzirio10
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Comment: C: diffHic ICE normalization PCA with NAs
... Hi Aaron, thanks for your reply!! Yes I'm doing the PCA for the A/B compartments... I'll do some more tests based on your comments! Thanks again, dario ...
written 7 months ago by inzirio10
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diffHic ICE normalization PCA with NAs
... Hi, I'm working with HI-C data and trying to compute the PCA loadings starting from the normalized contact matrix computed by correctedContact of the diffHic package, but I'm not able to do that because of the NAs produced during the normalization. Is there any way to avoid the NAs or to ignore th ...
normalization pca diffhic hi-c nas written 7 months ago by inzirio10 • updated 7 months ago by Aaron Lun25k
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Comment: C: Error : object path is not exported by namespace:Rsamtools
... Looking at NAMESPACEs of ensembldb and ensembldb, seems that they want to import this path function from Rsamtools package... But Rsamtools seems to not export it anymore!   ...
written 23 months ago by inzirio10
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Error : object path is not exported by namespace:Rsamtools
... Hi, from this morning this error appeared when I try to install some packages, like "ChIPpeakAnno" and "ensembldb". my sessioninfo is: sessionInfo() R Under development (unstable) (2017-11-26 r73782) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.3 LTS Matrix products: defau ...
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Comment: C: [DESeq2] time-course Experimental design
... Thank you very much for your answer! about your question: "I guess it's cost issues that are driving the question?" I'm trying to understand and capture different approaches to model the time course data analysis. So, for the (more complex) design, using DESeq2, didn't give me any problem, also be ...
written 2.3 years ago by inzirio10
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[DESeq2] time-course Experimental design
... I'd like to perform an experimental design for DESeq2 package using the LRT Test. I've already done it before using two different conditions Treated (T) vs Untreated (U), each at different time points. I was wondering how to design an experiment having the U replicates just at time point 0 and T r ...
rnaseq deseq2 time-course written 2.3 years ago by inzirio10 • updated 2.3 years ago by Gavin Kelly560

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