User: CantExitVIM

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CantExitVIM10
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Posts by CantExitVIM

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Limma without eBayes, is it indistunguishable from Ordinary Least Square?
... One post has caught my attention (https://support.bioconductor.org/p/35159/), which highlights how to "skip" the eBayes function. First, I understand that Bayes methodology is why limma is so popular and the benefits of utilizing such methods. But if one calculated the t-values and p-values as speci ...
bayesian limma ebayes ls written 6 days ago by CantExitVIM10 • updated 6 days ago by Gordon Smyth35k
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Comment: C: Limma: Don't have .CEL Affymatrix Files.
... Thank you for the quick reply, So there's no problem, you just read the matrix into R and use it in limma as usual. e_data <- read.table(file.path("file.txt"), skip=0, header=TRUE,sep="\t", row.names=1) e_data <- as.matrix(e_data) eSet_data <- ExpressionSet(e_data) exprs(eSet_data) <- ...
written 6 days ago by CantExitVIM10
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Limma: Don't have .CEL Affymatrix Files.
... I am working with Affymatrix ( U133A 2.0 chip) data for the first time. The data has been background corrected and normalized and intended to be used to compare different groups. From examining the e.coli Lrp example, I believe this data typically exists in the .CEL format with the mean expression l ...
limma affymetrix written 11 days ago by CantExitVIM10 • updated 10 days ago by Gordon Smyth35k
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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 9 weeks ago by CantExitVIM10
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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 4 months ago by CantExitVIM10 • updated 4 months ago by Gordon Smyth35k
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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 5 months ago by CantExitVIM10
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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 5 months ago by CantExitVIM10
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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 5 months ago by CantExitVIM10 • updated 5 months ago by Gordon Smyth35k
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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 7 months ago by CantExitVIM10
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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 7 months ago by CantExitVIM10 • updated 7 months ago by Gordon Smyth35k

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