User: RV

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RV10
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4 months, 3 weeks ago
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r*********************@covance.com

Posts by RV

<prev • 13 results • page 1 of 2 • next >
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Comment: C: HTA 2.0 Differential expression analysis - design question
... Thanks Aaron and James for the comprehensive answer. I really appreciate your help. ...
written 6 months ago by RV10
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Comment: C: HTA 2.0 Differential expression analysis - design question
... Hi James, Thank you! I have a couple more follow up questions and it will great to know your thoughts. > Assuming your call to makeContrasts is just a stylized version of what > you actually did (you presumably have more than one contrast of > interest, but obviously the entire call to m ...
written 6 months ago by RV10
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HTA 2.0 Differential expression analysis - design question
... Hi, I have 1500 HTA 2.0 affy human microarray CEL files. These file are a combination of treatment, placebo and healthy controls at 4 different times (weeks). They are not paired samples. Hence I started out doing the following - 1- Perform batch QC using Affy power tools 2- Perform sample wise QC ...
annotation affy limma hta written 6 months ago by RV10 • updated 6 months ago by James W. MacDonald51k
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Comment: C: Pre-processing of HTA 2.0 array
... Hi James, I did try all your above solution and my problem in any platform (I work on linux cluster with 250GB RAM, used a large ec2 instance with 1TB RAM) is that Oligo::rma gives me NaN's while processing all the files together. To eliminate the question of corrupt file, I divided the files into ...
written 7 months ago by RV10
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Comment: C: Oligo RMA normalization : ERROR; return code from pthread_create() is 22
... Hi Kevin, Apologies for the delayed reply. No, I am running it in a Red Hat server. It works just fine on a local command line. Thanks! ...
written 8 months ago by RV10
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Comment: C: Oligo RMA normalization : ERROR; return code from pthread_create() is 22
... Hi Kevin, Apologies for the delayed reply. No, I am running it in a Red Hat server. It works just fine on a local command line. Thanks! ...
written 8 months ago by RV10
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Comment: C: Arrayquality metrics Warning - Warning message in maximumLevels(fac, n = length(
... Hi Mike, arrayQualityMetrics(expressionset = Normdata_1, outdir = paste0("Normdata_1"), force = TRUE, intgroup = c("FUID","PLATE_ID","SCAN_DATE","VISIT","STATE","TRT01A")) I do not get any error for the last 3 values. The first thr ...
written 8 months ago by RV10
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Arrayquality metrics Warning - Warning message in maximumLevels(fac, n = length(colors)):
... Hi Wolfgang, I am using ArrayQuality metrics for more than 1300 samples and I get a warning - Warning message in maximumLevels(fac, n = length(colors)): "A factor was provided with 16 levels, but the colour map used here has only 9 colours. For the purpose of colouring, levels 9 ('1031863') to 16 ...
microarray wolfgang huber written 8 months ago by RV10
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Oligo RMA normalization : ERROR; return code from pthread_create() is 22
... I am trying to use oligo::rma for a HTA feature set from a linux environment and right after background correction, following is trace back – Background correcting Error in basicRMA(pms, pnVec, normalize, background): ERROR; return code from pthread_create() is 22 Traceback: ...
microarray normalization oligo hta written 9 months ago by RV10 • updated 3 months ago by jdshih20
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Array quality metrics for large sample size
... I am in the process of performing QC for > 1500 samples of HTA 2.0 array data. I am using oligo package and additional packages like arrayQualitymetrics to perform QC. I also using a linux system, and since most of these packages run single threaded - it takes a very a long time for all the proce ...
microarray quality written 9 months ago by RV10 • updated 8 months ago by Wolfgang Huber13k

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