User: tofukaj

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tofukaj0
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Posts by tofukaj

<prev • 13 results • page 1 of 2 • next >
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sva correction for MEDIPS
... Dear great R helpers, As mentioned in the post title, can surrogate variable (sva) batch correction in MeDIP-seq analysis using MEDIPS package? I must admit that I'm very new to such analysis and pretty poor at the concept. I would be deeply gratitude if someone could show me an example for such co ...
medips sva svaseq written 7 weeks ago by tofukaj0 • updated 7 weeks ago by Lukas Chavez490
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Comment: C: ChIPQC gives Error subscript contains out-of-bounds ranges with custom transcrip
... Thank you very very very much!!!!! ...
written 21 months ago by tofukaj0
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Comment: C: ChIPQC gives Error subscript contains out-of-bounds ranges with custom transcrip
... Dear Thomus, Thank you very much for your quick response. Since I'm an extreme newbie here, I really have no idea when you talk about peak.bed. All I have from MACS2 result is *.narrowpeak file. Here I provide you the link to all files I acquired from MACS. https://drive.google.com/file/d/0B4_V0v1 ...
written 21 months ago by tofukaj0
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ChIPQC gives Error subscript contains out-of-bounds ranges with custom transcript database
... Dear Great Helpers, I've tried 'ChIPQC' package with chip-seq data of the cow. I've created the annotation TxDb from 'gtf' file acquired from ensembl. The codes and results are as following: R library(GenomicRanges) library(GenomicFeatures) library(ChIPQC) # Create TxDb an ...
chipqc written 21 months ago by tofukaj0 • updated 21 months ago by Thomas Carroll400
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Comment: C: Is possible to apply 'svaseq' with 'DEXSeq' design in order to remove unknown ba
... Thank you very very much!! ...
written 2.1 years ago by tofukaj0
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Comment: C: Is possible to apply 'svaseq' with 'DEXSeq' design in order to remove unknown ba
... Thank you very much!! I hope this one looks ok for you. library( "DEXSeq" ) library( "DESeq2" ) library( "sva" ) inDir = system.file("extdata", package="pasilla") countFiles = list.files(inDir, pattern="fb.txt$", full.names=TRUE) basename(countFiles) flattenedFile = list.files(inDir, pattern="gff ...
written 2.1 years ago by tofukaj0
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Comment: C: Is possible to apply 'svaseq' with 'DEXSeq' design in order to remove unknown ba
... Dear Alejandro, I have tried svaseq analysis with  pasilla data in DEXSeq and have got an error. The script was as following library( "DEXSeq" ) library( "sva" ) inDir = system.file("extdata", package="pasilla") countFiles = list.files(inDir, pattern="fb.txt$", full.names=TRUE) basename(countFil ...
written 2.1 years ago by tofukaj0
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Comment: C: Is possible to apply 'svaseq' with 'DEXSeq' design in order to remove unknown ba
... Thank you very much, I will definitely have a look at the section you referred. ...
written 2.1 years ago by tofukaj0
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Is possible to apply 'svaseq' with 'DEXSeq' design in order to remove unknown batch effects ?
... Dear great R helpers, I would like to know if it is possible to apply 'svaseq' with 'DEXSeq' design in order to remove unknown batch effects similar to those greatly demonstrated with 'DESeq' (http://www.bioconductor.org/help/workflows/rnaseqGene/). Due to my poor background in bioinformatics and ...
dexseq svaseq written 2.1 years ago by tofukaj0 • updated 2.1 years ago by Alejandro Reyes1.6k
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Comment: C: How to use 'IHW' package to filter genes?
... Thank you very much for your great and very helpful answer!! ...
written 2.1 years ago by tofukaj0

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