User: n.lu

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n.lu0
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Posts by n.lu

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Diferential expresion analysis between different microarray platforms
... Hi, I was thinking about comparing my data set to other publicly available datasets, but they are not on the same platform (mine is Affymetrix Mouse Gene ST 2.0, the other ones are Affymetrix Mouse Gene ST 1.0 or Affymetrix Mouse Genome 430 2.0 Array.  I would be comparing samples from my arrays t ...
microarray platforms written 10 months ago by n.lu0
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Comment: C: Retrieving probes mapping to gene ID in microarray analysis
... Thank you!! Is it also possible to access their sequences? ...
written 11 months ago by n.lu0
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Comment: C: Retrieving probes mapping to gene ID in microarray analysis
... Thank you. That helps me get the probeset ID. Do you know if there is a way to go deeper than that and get all the probes that map to the probe set? I have Mouse Gene ST 2.0, I am particularly interested in "Fas" gene. The probe ID is 17358797, and I can see from the affymetrix  .csv file that the ...
written 11 months ago by n.lu0
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Retrieving probes mapping to gene ID in microarray analysis
... Hi,  How can one retrieve all the probes that map to a specific gene ID?  My data is form GeneChip™ Mouse Gene 2.0 ST Array, Affymetrix.    ...
microarray probe affymetrix probeset written 11 months ago by n.lu0 • updated 11 months ago by Mike Smith2.9k
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Comment: C: Quality control for Affymetrix GeneChip Mouse Gene 2.0 ST Array
... Thank you for your answer! Best, Nina ...
written 13 months ago by n.lu0
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Quality control for Affymetrix GeneChip Mouse Gene 2.0 ST Array
... Hi,  I am trying to analyze data from Affymetrix GeneChip Mouse Gene 2.0 ST Array. I am using "oligo" package to import .CEL files, preprocess and do QC, but I noticed that oligo package has a limitted selection of QC stats compred to simpleAffy and affyQCReport (which I cant use because I cant imp ...
qualitycontrol arrayqualitymetrics affymetrix qc mouse gene st 2.0 written 13 months ago by n.lu0 • updated 13 months ago by James W. MacDonald47k
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Comment: C: Nonspecific filtering of microarray data
... Thank you!   ...
written 15 months ago by n.lu0
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Comment: C: Nonspecific filtering of microarray data
... My experiment has 4 groups - 2 different genotypes- wild type and a knockout - and then in both a group with disease and a control (WT control, WT disease, knockout disease, knockout control). I want to do analysis of differentaly expressed genes between these groups, and than add some pathway analy ...
written 15 months ago by n.lu0
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Nonspecific filtering of microarray data
... Hi, I am quite new to this field. Does anybody have recomendations on the criteria to use for prefiltering genes in genefilter package? I have found a few of them (row SDS, IQR, intensity based filtering) but am not sure which one/what combination to use. Or should I not prefilter at all?     ...
microarray filtering pre-filtering affymetrix microarrays nonspecific filtering written 15 months ago by n.lu0 • updated 15 months ago by Wolfgang Huber13k

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