User: rbenel

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rbenel0
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Posts by rbenel

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Comment: C: Constructing tx2gene for Salmon txImport Quantification using Gencode Mouse Tran
... Yes, after using the sub(".*", "",\\|) workaround I ended up re-quantifying my files, this time with the --gencode argument as well as --keepDuplicates since I am interested in transcript analysis. Thanks!      ...
written 10 days ago by rbenel0
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Comment: C: Constructing tx2gene for Salmon txImport Quantification using Gencode Mouse Tran
... Thanks! Is this argument using strsplit? I want to use a wrapper function that utilizes tximport with gencode annotations, but it is not updated for the "ignoreAfterBar" argument.. Update: Your function uses sub("\\|.*", "",) ...
written 13 days ago by rbenel0
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Comment: C: Constructing tx2gene for Salmon txImport Quantification using Gencode Mouse Tran
... Hi Michael,  I would also really like to use the "ignoreAfterBar", but I receive an error saying it is an used argument... I do not know how long this parameter has been around, so this may be partially due to the fact that my current tximport version is set up as 1.6.0 but I can't seem to update t ...
written 14 days ago by rbenel0 • updated 14 days ago by Michael Love19k
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Comment: C: DESeq2 Normalized Counts for Mfuzz
... Just to update anyone who might be interested in using the Mfuzz package on normalized DESeq2 counts:  From the developers of Mfuzz: "For RNA-seq, you could input log-transformed normalised cpm and then use the standardise function. If you are looking specifically for peaks, you can spare the log t ...
written 22 days ago by rbenel0
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Comment: C: DESeq2 Normalized Counts for Mfuzz
... OK, thanks for the input. I tagged Mfuzz as well, but not every developer is as active as you are ;)  On the topic of downstream analysis and normalized counts, if I wanted to look at the correlation between genes, (at the expression level), is using one of the transformed counts appropriate?  as ...
written 23 days ago by rbenel0
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Comment: C: DESeq2 Normalized Counts for Mfuzz
... OK. This specific method wants normalized counts, and since the sample size is n < 30, in the vignette you suggest to use rlog.  So if my design = ~ replicate + day it is in my best interest to use mat <- assay(rld)  mat2 <- removeBatchEffect(mat, rld$replicate)?  and ​then use mat2 as an ...
written 23 days ago by rbenel0
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DESeq2 Normalized Counts for Mfuzz
... Hi,  I would like to preform temporal patterning using the package Mfuzz which assumes the given expression data are fully pre-processed including data normalization and averaging of replicates.  As @Michael Love explained in this question https://support.bioconductor.org/p/87999/ "the normalized ...
rnaseq mfuzz deseq2 written 23 days ago by rbenel0 • updated 23 days ago by Michael Love19k
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Comment: C: Visualization for Time Course "LRT" test in DESeq2
... I have a follow up question... as I am still looking for a visualization method for all deferentially genes at once. What if I compute all pairwise comparisons using test = "Wald", and I represent this as a heatmap of differential expressed genes in at least one time point. If there added value in r ...
written 5 weeks ago by rbenel0
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Comment: C: Error in Apeglm Method for Effect Size Shrinkage
... OK. I successfully installed REBayes, but users should know that it has dependencies to Rmosek, which requires instillation of mosek to one's local computer, which requires a license... so it was a bit of a long process to install the REBayes package.  Thanks! ...
written 5 weeks ago by rbenel0
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Comment: C: Error in Apeglm Method for Effect Size Shrinkage
... Hi Michael,  Here are the dimension of the model: dim(model.matrix(design(dds), colData(dds))) [1] 32 13 type = "ashr" gives me this type of warning message:  Due to absence of package REBayes, switching to EM algorithm I have tried to install the REBayes package, but I am currently having is ...
written 6 weeks ago by rbenel0

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