User: alerodriguez

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Posts by alerodriguez

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error when trying to apply the specific gene filter.
... Please help me understand why I get an error when trying to apply the specific gene filter. Please see details below: I am working with microarray data  dim()=54675    80 grouped by status table(gcrma.ExpressionSet$TG.binary) =group1=52 and group2=28 My data is in log2  #---------------------spe ...
genefilter written 3 days ago by alerodriguez0 • updated 2 days ago by James W. MacDonald43k
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Comment: C: Non-specific filtering methodogies for ExpressionSet in R/Bioconductor
... I apologize, I'm very new to microarray data analysis would you please elaborate on the meaning of "mean log-expression".Thanks     ...
written 5 days ago by alerodriguez0
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removing batch effects using sva combat and linear regression
... After using comBat to remove know batch effects, I used sva to estimate unknown sources of variation. I saved the surrogate variables to my phenotype file and regress these variables along with other covariates as shown in the formula. x=lm(loc2[,i]~Age+Sex+surrogate.1+surrogate.2+batch, data=pData ...
combat sva microarry jeff leek written 6 days ago by alerodriguez0
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Comment: C: SVA: Including variable of interest in ComBat model matrix
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written 6 days ago by alerodriguez0
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Comment: C: Error in TOMplot (WGCNA)
... Abhishek,  Did you ever get a response from the authors? Thanks!         ...
written 5 weeks ago by alerodriguez0
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Comment: C: expression correlation on an ExpressionSet
... Thanks!  I was told that to do an expression correlation (case/control) all I needed was Excel. Can you give me your thoughts about my approach, I started with .txt files and build an ExpressionSet ( is this what people normally do?) I did this because reading the Affy and other vignettes I was able ...
written 5 months ago by alerodriguez0
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Answer: A: expression correlation on an ExpressionSet
... I want to know if the expression of all genes in the controls differs from those in the cases.  I would like to visualize this with a heat map.     ...
written 5 months ago by alerodriguez0
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expression correlation on an ExpressionSet
... Hi, I have .txt files with phenotype data and expression values from an Affymetrix microarray. I constructed an ExpressionSet class from scratch. I need to generate and plot an expression correlation matrix for all genes comparing case vs control.I'm very new to R and Bioconductor and would greatly ...
plot expressionset correlation casecontrol written 5 months ago by alerodriguez0 • updated 9 weeks ago by vulegom0

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