diff --git a/RPR-GEO2R.R b/RPR-GEO2R.R index 5003dd8..e5786a9 100644 --- a/RPR-GEO2R.R +++ b/RPR-GEO2R.R @@ -34,6 +34,7 @@ #TOC> #TOC> Section Title Line #TOC> -------------------------------------------------------------------- +<<<<<<< HEAD #TOC> 1 Preparations 53 #TOC> 2 Loading a GEO Dataset 84 #TOC> 3 Column wise analysis - time points 154 @@ -46,6 +47,20 @@ #TOC> 5.1 Final task: Gene descriptions 490 #TOC> 6 Improving on Discovery by Differential Expression 495 #TOC> 7 Annotation data 577 +======= +#TOC> 1 Preparations 51 +#TOC> 2 Loading a GEO Dataset 82 +#TOC> 3 Column wise analysis - time points 152 +#TOC> 3.1 Task - Comparison of experiments 158 +#TOC> 3.2 Grouped Samples 205 +#TOC> 4 Row-wise Analysis: Expression Profiles 240 +#TOC> 4.1 Task - Read a table of features 275 +#TOC> 4.2 Selected Expression profiles 323 +#TOC> 5 Differential Expression 364 +#TOC> 5.1 Final task: Gene descriptions 488 +#TOC> 6 Improving on Discovery by Differential Expression 493 +#TOC> 7 Annotation data 575 +>>>>>>> b17a9e202ad3429a716683538b3d0ed8d7d9ff9e #TOC> #TOC> ========================================================================== @@ -586,6 +601,7 @@ GSE3635annot <- getGEO("GSE3635", GSEMatrix = TRUE, getGPL = TRUE) GSE3635annot <- GSE3635annot[[1]] # ... and the feature data is then available in the GSE3635@featureData@data +<<<<<<< HEAD # slot: str(GSE3635annot@featureData@data) GSE3635annot@featureData@data[ 1:20 , ] @@ -610,6 +626,13 @@ myAnnot[which(myAnnot$Gene == "MBP1"), ] # Alternatively, we could have identified the GPL file for this set: +======= +# slot: +str(GSE3635annot@featureData@data) +GSE3635annot@featureData@data[ 1:20 , ] + +# ... or we could have identified the GPL file for this set: +>>>>>>> b17a9e202ad3429a716683538b3d0ed8d7d9ff9e GSE3635@annotation # "GPL1914" # ... and downloaded it directly from NCBI: @@ -617,9 +640,13 @@ GPL1914 <- getGEO("GPL1914") str(GPL1914) # ... from which we can get the data - which is however NOT necessarily +<<<<<<< HEAD # matched to the rows of our expression dataset. Note that here to: the majority # of data elements are factors and will likely have to be converted before # use. +======= +# matched to the rows of our expression dataset. +>>>>>>> b17a9e202ad3429a716683538b3d0ed8d7d9ff9e # [END]