User: andrebolerbarros

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Posts by andrebolerbarros

<prev • 28 results • page 1 of 3 • next >
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Comment: C: z-score with DESeq2?
... Thanks Michael. So, the procedures would be to perform Z-score on the rlog-transformed data? André ...
written 3 months ago by andrebolerbarros10
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Comment: C: estimateSizeFactors after subsetting?
... Thanks Michael, for your response. I've looked at the vignette, and indeed found the scenario for when to subset. However, in the context of a subset, do the `estimateSizeFactors` be run *a priori*, before running DESeq again? ...
written 5 months ago by andrebolerbarros10
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estimateSizeFactors after subsetting?
... Hello everyone, I have a dataset of RNASeq counts for several cell types. For each cell type, I am running a DESeq model for the specific subset. Should I run `estimateSizeFactors` for each subset or use the global one? Example: dds<-DESeq(dds) dds_sub<-dds[dds$condition!="CellA",] ...
deseq2 written 5 months ago by andrebolerbarros10 • updated 5 months ago by Michael Love26k
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z-score with DESeq2?
... Hello everyone, Do you know if it's possible to use Z-score values for counts normalized using DESeq2? My main objective is to get mean values of gene expression for several populations, mainly for visualization objectives. Thanks in advance, André ...
deseq2 written 7 months ago by andrebolerbarros10 • updated 7 months ago by Michael Love26k
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Comment: C: Using vegan::betadisper for determing if I subset my design for DESeq2
... Thanks for the feedback! I got the idea from amplicon sequencing analysis, where they normally use PERMANOVA and, consequently, the `betadisper` functions. This could be a good addition to help users to know if the groups have similar variances, besides EDA. ...
written 7 months ago by andrebolerbarros10
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Using vegan::betadisper for determing if I subset my design for DESeq2
... Hi everyone, I'm currently analyzing a RNA-Seq data using DESeq2. Looking at the FAQ's in https://www.bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html, concerning the subset of data, the authors recommend "users to run samples from all groups together, and then use the con ...
deseq2 written 7 months ago by andrebolerbarros10 • updated 7 months ago by Michael Love26k
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Comment: C: DESeq2 for QuantSeq data
... Thanks for your response! I asked that because I was searching for QuantSeq and found this link: https://rpubs.com/chapmandu2/171024 I'll try with DESeq2 then. Thank you! ...
written 8 months ago by andrebolerbarros10
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DESeq2 for QuantSeq data
... Hi everyone, I've received data from RNA-Seq from my facility, which was sequenced using QuantSeq Kit. In theory, this kit allows for differential expression analysis cost-efficiently and with lower sequencing depth (less than 10M per sample, in comparison with some samples I got before, which had ...
deseq2 written 8 months ago by andrebolerbarros10 • updated 8 months ago by cats_dogs20
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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 12 months ago by andrebolerbarros10 • updated 12 months ago by Michael Love26k
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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 13 months ago by andrebolerbarros10 • updated 13 months ago by Michael Love26k

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