User: assaf www

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assaf www140
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Posts by assaf www

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Comment: C: can KEGG figures produced by pathview be used in publication, or that they are c
... thanks, Heyi ...
written 13 months ago by assaf www140
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can KEGG figures produced by pathview be used in publication, or that they are copyrighted ?
... Dear Pathview and Clusterprofiler developers, During a submission process of a manuscript, which includes KEGG figures produced by via pathview (based on the functional enrichment results found using Clusterprofiler and Goseq) we are specifically asked to provide a permission for the usage of the f ...
clusterprofiler pathview written 13 months ago by assaf www140
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Comment: C: EdgeR GLM, when factor categories are not equaly represented in different groups
... Hi Gordon, In fact EdgeR gave a relatively large group of genes in which the effect of treatmentB was significant, especially for the treatmentB_0 vs. treatmentB_2 groups. I tried to visualized it by grouping the samples by Batch and TreatmentA (so, the same categories appear in each group), and th ...
written 14 months ago by assaf www140
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EdgeR GLM, when factor categories are not equaly represented in different groups
... Hi EdgeR developers and all, I'm testing RNA-Seq data with the following factors: treatmentA , with the categories 0,1 treatmentB ,  with the categories 0,1,2 batch , with the categories 0,1,2,3 the goal is to detect genes in which the effect of treatmentA, and (separately) the effect of treatmen ...
edger written 14 months ago by assaf www140 • updated 14 months ago by Gordon Smyth32k
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Comment: C: how to incorporate count bias in Goseq
... Thanks a lot, It's not so clear from the manual though, but if so then best option would be to choose any gene parameter with the highest correlation with the DE proportion, as long as such parameter is technical (does not represent true biological factor). Assaf ...
written 14 months ago by assaf www140
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how to incorporate count bias in Goseq
... Dear goseq developers and all, Following the question here https://support.bioconductor.org/p/60759 The code in Goseq manual says: countbias=rowSums(counts)[rowSums(counts)!=0] pwf.counts=nullp(genes,bias.data=countbias) It appears the input to nullp should be the sum of the raw read counts per-g ...
edger goseq written 15 months ago by assaf www140 • updated 15 months ago by anthony.hawkins10
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read-count normalization and mRNA degradation in Deseq2 and EdgeR
... Deseq and EdgeR developers and user hi, I'm testing an RNA-Seq data set for few developmental time-points (t0,t4,t12,t18,t21,t24,t48) with no replicates (more details here: https://support.bioconductor.org/p/75773/#75851). All samples come from the same embryos culture, and can be considered as sam ...
edger deseq2 written 21 months ago by assaf www140 • updated 21 months ago by Michael Love15k
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Comment: C: Limma Voom and quadratic regression
... Are the treatment individuals the same as the control individuals? the answer is positive, at least at this point (we have only sequenced a pilot experiment yet, but will expand that) more specifically, these are not people but embryo cultures, where each culture is composed of thousands of embryo ...
written 23 months ago by assaf www140
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Comment: C: Limma Voom and quadratic regression
... Hi Gordon, and Aaron, OK, so I understand how to compare the null model (no spline), and the alternative one, at least in this simple setting with no paired design, and, in order to plot the fit for a given gene, the 4 values of its fit (intercept,x1,x2,x3) are multiplied by the corresponding 4 val ...
written 23 months ago by assaf www140 • updated 23 months ago by Gordon Smyth32k
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Comment: A: Limma Voom and quadratic regression
... Hi Aaron, So, the design is partitioned to 3 layers: 1) genes count measurements taken from a single individual at x time points (currently x= 0  4 12 18 21 24 48 hours). 2) the above experiment is repeated n times, for n different individuals, to give n*x samples 3) the above is repeated 2 time ...
written 23 months ago by assaf www140

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