User: S. K.

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S. K.0
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Germany, Heidelberg
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3 months, 3 weeks ago
Joined:
8 months ago
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s***@kernelspace.de

Posts by S. K.

<prev • 7 results • page 1 of 1 • next >
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Comment: C: beadarray: readIllumina with sample sheet broken due to Illumina switching to 12
... Additionally, this is the structure of the zipped folders I receive from our core facility: 2017-03-16 18:43:25 ....A 1340 1024119382 200647550006/200647550006_A_Green.xml 2017-03-16 18:43:14 ....A 1316 200647550006/200647550006_A_Red.xml 2017-03-16 18:43:52 ....A ...
written 7 months ago by S. K.0
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Comment: C: beadarray: readIllumina with sample sheet broken due to Illumina switching to 12
... Hi Mark, thanks for your reply! I managed to get it working - at least as long as I don't specify useImages in readIllumina().  I had to change summarize() as well, the attached diffs work for my dataset (see below), though I can't say anything about backward compatibility with older, shorter chi ...
written 7 months ago by S. K.0
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Answer: A: beadarray: readIllumina with sample sheet broken due to Illumina switching to 12
... I looked at readIllumina.R in more detail and it seems that the condition for the if statement in line 82 always evaluates to FALSE due to misplaced parentheses? Currently it's written as: if(all(nchar(allSections))>10){ chips <- unique(as.character(substr(allSections,1,nchar(al ...
written 7 months ago by S. K.0
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Comment: C: beadarray: summarizing iScan data is not working
... Just a wild guess but might be related to another problem of mine due to longer chip identifiers since last October: http://support.bioconductor.org/p/95307/ ...
written 7 months ago by S. K.0
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beadarray: readIllumina with sample sheet broken due to Illumina switching to 12 digit chip identifiers
... Hi, I am still trying to get beadarray's readIllumina() working with recently acquired data from HT-12 v4 beadchips and using a sample sheet. No matter what I was trying in that sample sheet, I always got: Error in analyseDirectory(dir = x, sectionNames = as.character(dirs[[x]]), : Directory ...
beadarray bug illumina beadchip illumina human ht-12 v4 written 7 months ago by S. K.0 • updated 7 months ago by Mark Dunning1.1k
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beadarray: summarizing iScan data is not working
... Hello, I am trying to read Illumina HT12-v4 beadarrays with beadarray that were scanned with an iScan system. All necessary files are residing in the current working directory and I am not using a sample file. library(beadarray) processSwathData() ExpBData <- readIllumina(illuminaAnnotation = ...
beadarray iscan written 8 months ago by S. K.0
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beadarray: Make grep in readSamplesheet case insensitive
... Hi, I was having trouble reading my samplesheet from a recent iScan-run of HumanHT12 chips with beadarray and noticed this is probably due to readSamplesheet not grepping case insensitive for [Header] and [Data], so [HEADER] (which was in the file I received) is not found and results in the error: ...
beadarray bug written 8 months ago by S. K.0

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