User: andrebolerbarros

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Posts by andrebolerbarros

<prev • 20 results • page 1 of 2 • next >
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When should I use betaprior=T
... Hi everyone, I have RNASeq Data, with 4 conditions, 2 replicates each (very far from ideal, I know). By looking at my data through heatmap and PCA, I see that there are relevant differences within conditions, among replicates. To further analyze this dataset, I got the recommendation of using beta ...
deseq2 written 5 days ago by andrebolerbarros0 • updated 5 days ago by Michael Love20k
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alpha in lfcshrink?
... Hi everyone, In DESeq2, we can optimize the independent filtering step in calculating the results by changing alpha. Is there a way to perform that as well for lfcshrink? Thanks! ...
deseq2 written 23 days ago by andrebolerbarros0 • updated 23 days ago by Michael Love20k
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Comment: C: Pre-filtering results influence on downstream analysis
... It's what I suspected, thanks! Then, what criteria for pre-filtering should I use? ...
written 23 days ago by andrebolerbarros0
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Pre-filtering results influence on downstream analysis
... Hello everyone, I am currently working on RNA-Seq data using DESeq2. As it is in the manual, you can perform pre-filtering (e.g.: keep <- rowSums(counts(dds)) >= 10 dds <- dds[keep,] However, it's also said that: "While it is not necessary to pre-filter low count genes before running th ...
rnaseq deseq2 written 23 days ago by andrebolerbarros0 • updated 23 days ago by Michael Love20k
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Comment: C: Import_biom with tree problem
... Solved in phyloseq github; Issue #408: Removing the label-row from list file solved the problem ...
written 7 weeks ago by andrebolerbarros0
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Import_biom with tree problem
... Hey! I'm trying to import my mothur data in phyloseq, by first of all import the list, group and tree files: phyl<-import_mothur(mothur_list_file = "total.final.pick.opti_mcc.list", mothur_group_file="total.final.pick.groups", mothur_tree_file = "total.final.pick.tre") However, I get an er ...
phyloseq 16s mothur written 7 weeks ago by andrebolerbarros0
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Comment: C: DESeq2 - Differences between plotCounts and normalized counts
... The difference is consistently 0.5, which corresponds to the default value for pseudo-counts in plotCounts, that was my first assumption. ...
written 3 months ago by andrebolerbarros0
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Comment: C: DESeq2 - Differences between plotCounts and normalized counts
... Here they are:        counts group 1 2147.32347 A 2 2784.83020 A 3 5149.40495 A 4 4873.66509 A 5 1754.78676 A 6 4466.54202 B 7 1832.26189 B 8 1795.62376 B 9 659.41229 B 10 736.23997 B 11 35.24922 C 12 35.52343 C 13 35.46535 C ...
written 3 months ago by andrebolerbarros0
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Comment: C: DESeq2 - Differences between plotCounts and normalized counts
... Let's imagine I have gene A. When I perform plotCounts, the output consistis of a data.frame: count group 1 2147.82347 A 2 2785.33020 A 3 5149.90495 A 4 4874.16509 A 5 1755.28676 A 6 4467.04202 B 7 1832.76189 B 8 1796.12376 B 9 659.91229 B 10 7 ...
written 3 months ago by andrebolerbarros0
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Comment: C: DESeq2 - Differences between plotCounts and normalized counts
... As far as I understand then, the values I get from plotCounts are different since the processing of the data by DESeq2 is more complicated than "just" normalization by sequencing depth. Is there any way to access the values for the values used for DESeq2 calculations? The main objective of this is ...
written 3 months ago by andrebolerbarros0

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