User: rbenel

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rbenel0
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Posts by rbenel

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Plotting Expression of Differential Transcripts following DEXSeq and StageR
... Hi,  I was wondering which counts are appropriate to use for plotting the expression of the differential transcripts? plotDEXSeq is giving me this error:  Error in plot.window(xlim = c(0, 1), ylim = c(0, max(matr))) : need finite 'ylim' values In addition: Warning messages: 1: In max(coeff, na ...
dexseq dtu stager written 2 days ago by rbenel0
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Comment: C: Graphically Represent p-values from plot_annot_score in package GOfuncR
... Hi Steffi,  Thanks for the response. I didn't realize that is what you meant by "invisible".. thanks for clarifying. ...
written 16 days ago by rbenel0
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Graphically Represent p-values from plot_annot_score in package GOfuncR
... In the tutorial it mentions that plot_anno_scores returns an invisible dataframe that contains the stats from Fisher’s exact test shown in the plot. I was wondering if there was a way to extract this dataframe? It would also be helpful if one could manipulate the plot... for example, I would like to ...
gofuncr plot_anno_scores plot_stats written 20 days ago by rbenel0 • updated 19 days ago by steffi_grote0
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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 weeks 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 11 weeks 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 11 weeks ago by rbenel0 • updated 11 weeks 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 12 weeks 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 12 weeks 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 12 weeks 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 12 weeks ago by rbenel0 • updated 12 weeks ago by Michael Love19k

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