User: tangboyun

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tangboyun30
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China
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3 years, 2 months ago
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4 years, 10 months ago
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t********@hotmail.com

Posts by tangboyun

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The current annotation for Affymetrix HTA 2.0 array is problematic
... It seems that Affy is silently changing their procedure for the probeset annotation of HTA 2.0. cut -d"," -f 1,10,13 HTA-2_0.na33.hg19.probeset.csv "probeset_id","psr_id","probeset_type" "2824546_st","2824546_st","normgene->exon" "2824549_st","2824549_st","normgene->exon" "2824551_st","2824 ...
oligo pdinfobuilder pd.hta.2.0 written 4.2 years ago by tangboyun30
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Confused by the probe design of Affymetrix Human Transcriptome Array (HTA 2.0)
... Dear List,      I 'm developing a pipeline for analysing the HTA 2.0 chips. It works smoothly if I use the default settings of the rma function in the oligo package. But when I try to add some extra procedures for bg corrections of the non-specific binding  using the probe informations, I found som ...
microarray normalization oligo written 4.9 years ago by tangboyun30 • updated 3.8 years ago by burchard0
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Comment: C: Trouble with gcrma, Segfault on background correction
... You are right. Thank you very much.  By the way, I found a list of probes in the primeview array design and also a paper (http://europepmc.org/articles/PMC3683922) using thses probes for bg ctrl.  [1] "AFFX-BkGr-GC03_at" "AFFX-BkGr-GC04_at" "AFFX-BkGr-GC05_at" [4] "AFFX-BkGr-GC06_at" "AFFX-BkGr ...
written 4.9 years ago by tangboyun30
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Trouble with gcrma, Segfault on background correction
... Dear list, I try to run gcrma using the affinity computation without taking into account MM probes, and following commands lead to segfault.   > library(simpleaffy) > rawData <- ReadAffy() # Read in PrimeView CELs (no MM probes) > eset <- gcrma(rawData, affinity.info=compute.aff ...
affy gcrma written 4.9 years ago by tangboyun30 • updated 4.9 years ago by James W. MacDonald51k

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Popular Question 4.1 years ago, created a question with more than 1,000 views. For Confused by the probe design of Affymetrix Human Transcriptome Array (HTA 2.0)

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