User: lech.kaczmarczyk

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Posts by lech.kaczmarczyk

<prev • 9 results • page 1 of 1 • next >
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Comment: C: Error in summary.DESeqResults(res) : could not find function "summary.DESeqResu
... Tried to install it from source, but it did not solve the problem... ...
written 3 months ago by lech.kaczmarczyk10
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Comment: C: Error in summary.DESeqResults(res) : could not find function "summary.DESeqResu
... > BiocManager::valid("DESeq2") [1] TRUE Should I install it some other way than with `BiocManager()`? ...
written 3 months ago by lech.kaczmarczyk10
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Error in summary.DESeqResults(res) : could not find function "summary.DESeqResults"
... I'm trying to run DESeq2 but got stud on this error: using pre-existing size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship -- note: fitType='parametric', but the dispersion trend was not well captured by the function: y = a/x + ...
deseq2 written 3 months ago by lech.kaczmarczyk10 • updated 3 months ago by Michael Love25k
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Comment: C: Removing batch effect with limma::removeBatchEffect() actually exacerbates the e
... Many thanks for your response Michael, I appreciate that. This was RNAseq of mouse brain regions- and cell-specific RNA immunoprecipitations. Groups denote the days the mice were sacrificed. Conditions were not divided further. Since the outliers were overlapping with the time-points in which the s ...
written 4 months ago by lech.kaczmarczyk10
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Removing batch effect with limma::removeBatchEffect() actually exacerbates the effect
... ![enter image description here][1]Hello, I am attempting to remove batch effects from my data using `limma::removeBatchEffect()`. I have two batches of samples, and there are four conditions. In the figures below batches are color-coded. I'm wondering why the batch effect seems stronger after apply ...
limma deseq2 written 4 months ago by lech.kaczmarczyk10 • updated 4 months ago by Gordon Smyth39k
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Comment: C: Importing transcript abundance datasets generated with Salmon 0.14.0
... OK, I reinstalled it and now it's working! Thanks again Michael! ...
written 4 months ago by lech.kaczmarczyk10
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Comment: C: Importing transcript abundance datasets generated with Salmon 0.14.0
... R version 3.6.0 (2019-04-26) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Mojave 10.14.5 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library ...
written 4 months ago by lech.kaczmarczyk10
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Comment: C: Importing transcript abundance datasets generated with Salmon 0.14.0
... Getting the same error, is there any quick fix? Thanks ML for working on it. ...
written 4 months ago by lech.kaczmarczyk10
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Custom graphNEL object for pathview
... Hi All, I would like to compare miRNA and mRNA sequencing results using Pathview. By default, Pathview uses a KEGG xml file downloaded using the function pathview(). My first problem is how to feed Pathview with a custom pathway (for example a reactome pathway converted into graphNEL object)? I am ...
mirna pathview mirintegrator written 2.0 years ago by lech.kaczmarczyk10

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