User: nicolas.descostes

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Posts by nicolas.descostes

<prev • 8 results • page 1 of 1 • next >
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Answer: A: soGGi package: Error in .validate_names(rownames, ans_rownames, "assay rownames(
... Adding this line to the code solved the issue: ``` profileMat <- RegionsMat colnames(profileMat) <- c(paste0("Point_Centre",seq(0-distanceUpStart,-1)),"Point_Centre",paste0("Point_Centre",seq(1,distanceDownEnd))) filteredRanges <- c(RangesPos,RangesNeg) -------> ****names(fi ...
written 5 months ago by nicolas.descostes20
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soGGi package: Error in .validate_names(rownames, ans_rownames, "assay rownames()"
... Hi, I am following this tutorial: https://rockefelleruniversity.github.io/RU_ATAC_Workshop.html I tried the most recent version of soGGi but also the one of the tutorial (1.10.4). When calculating: ``` nucFree <- regionPlot(bamFile = sortedBAM, testRanges = TSSs, style = "point", format ...
soggi written 5 months ago by nicolas.descostes20
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Answer: A: masigpro: could not find function "negative.binomial"
... ok it is working now. Thank you for the correction. ...
written 10 months ago by nicolas.descostes20
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masigpro: could not find function "negative.binomial"
... Hi, After updating to bioconductor 3.8, I have some troubles using p.vector. The command and error are: > fit <- p.vector(edgeR_cpm_matrix, design, Q = 0.05, MT.adjust = "BH", counts=TRUE, family= negative.binomial(10)); Error in negative.binomial(10) :   could not find function "negative.bi ...
masigpro written 10 months ago by nicolas.descostes20
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Comment: C: normalization of ChIP-seq data
... you can also have a look at chipseqspike if you used spike-in controls ...
written 10 months ago by nicolas.descostes20
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Comment: C: csaw: Estimate fragment length
... thanks a lot! ...
written 18 months ago by nicolas.descostes20
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csaw: Estimate fragment length
... Hi, I have been following the csaw vignette and this article: https://f1000researchdata.s3.amazonaws.com/manuscripts/8237/a7de2136-b076-43a6-9376-7eec24c7d4117016-_Aaron_Lun_V2.pdf?doi=10.12688/f1000research.7016.2 For estimating the fragment length, two commands are suggested: maximizeCcf (in the ...
csaw written 18 months ago by nicolas.descostes20
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maSigPro error PlotGroups [Error: (list) object cannot be coerced to type 'double']
... Dear members, I am going through an error in the function PlotGroups called itself from the function see.genes. The error says: Error: (list) object cannot be coerced to type 'double' Looking at the code, the error is coming from the first "if" condition when performing a conversion to numeric: ...
masigpro error plotgroups written 2.3 years ago by nicolas.descostes20

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Popular Question 2.2 years ago, created a question with more than 1,000 views. For maSigPro error PlotGroups [Error: (list) object cannot be coerced to type 'double']

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