User: CantExitVIM

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Posts by CantExitVIM

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Finding/Understanding Affy 6.0 Annotation File
... First, I apologize if this is a stupid question. I am a grad-student and this is the first-time working with such data. Per individual, I have 4,257,405 SNP probes from chromosomes 1-22. All these probes are recorded by their  dbSNP RS IDs (e.g. rs13031737, rs62116682, etc). Some of the probes have ...
snp microarray affy affymetrix written 7 days ago by CantExitVIM0
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Why does backgroundCorrect with method="none" produce different plots with plotMA()?
... Code Snippet: x <- read.maimages(targets,source="agilent", green.only=TRUE) plotMA(x) ybc <-backgroundCorrect(x, method="none") plotMA(ybc)   If I use plotMA3by2(), I get the same results. This is expected since no background correction was done (method = "none"). But for some reason, plot ...
agilent background correction plotma single channel written 10 weeks ago by CantExitVIM0 • updated 10 weeks ago by Gordon Smyth34k
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Comment: C: Agilent Single-Channel Data: Questions about model statement and model building.
... So... yea... that's probably an indication that I should get some sleep. Thanks again =) ...
written 3 months ago by CantExitVIM0
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Comment: C: Agilent Single-Channel Data: Questions about model statement and model building.
... Thank you for the feedback. Follow up Question: I want topTable() to show the regression slopes. Seeing that this is not an option in the documentation, I need to extract slopes from the MArrayLM object and pertinent information from topTable. unsortedTT <-topTable(fit, n=Inf, coef=2, sort.by= ...
written 3 months ago by CantExitVIM0
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Agilent Single-Channel Data: Questions about model statement and model building.
... I am attempting to analyze single-channel Agilent micro array data from two different groups. I have numerous covariates for each individual within these groups and have specified categorical covariates using the factor() method. Sex <- targets[,"Sex"] #Note: targets is the target file containi ...
microarray limma agilent covariates written 3 months ago by CantExitVIM0 • updated 3 months ago by Gordon Smyth34k
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Comment: C: Agilent One Channel Data: Will I be able to use limma with flagged data removed.
... I think you are correct and I probably was misinterpreting what was being asked. If I remove/keep individual probes based on gIsWellAboveBG... I am creating a bunch of data-sets that can't be compared. Based on your comment, I suspect he wanted me to remove probes that are universally "poor" in all ...
written 5 months ago by CantExitVIM0
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Comment: C: Agilent One Channel Data: Will I be able to use limma with flagged data removed.
... As you probably inferred from my first post, I understand that I am not following standard practices. And I hope this isn't interpreted as some brash disregard of thoughtful and tested practices. Long story short, I am bioinformatics grad student that is trying my best to analyze Agilent one-channel ...
written 5 months ago by CantExitVIM0 • updated 5 months ago by Gordon Smyth34k
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Comment: C: Agilent One Channel Data: Will I be able to use limma with flagged data removed.
... I would like to conduct normalization with probe values that have a "gIsWellAboveBG" value of 1 and ignore/extract probes with a value of 0. ...
written 5 months ago by CantExitVIM0
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Comment: C: Agilent One Channel Data: Will I be able to use limma with flagged data removed.
... I broke the code down in order to understand it. I am sure much of the confusion stems from me being new to R. But I don't understand (1) what values are being passed to that function, (2) how weights are being assigned, and (3) how that information is being fed-back into read.maimages. For instanc ...
written 5 months ago by CantExitVIM0 • updated 5 months ago by Gordon Smyth34k
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Comment: A: Agilent One Channel Data: Will I be able to use limma with flagged data removed.
... "You simply read the microarray data into limma in the normal way, then set all the spots that are flagged to have zero weights Then all flagged spots will automatically be removed from any limma downstream analysis."  I was playing around with some code that I found in another thread ( https://sup ...
written 5 months ago by CantExitVIM0 • updated 5 months ago by Gordon Smyth34k

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