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Merge branch 'master' of https://github.com/hyginn/ABC-units

# Conflicts:
#	RPR-GEO2R.R
This commit is contained in:
hyginn 2018-01-28 18:49:24 -05:00
commit c17b340b38
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RPR-GEO2R.R
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@ -34,6 +34,7 @@
#TOC> #TOC>
#TOC> Section Title Line #TOC> Section Title Line
#TOC> -------------------------------------------------------------------- #TOC> --------------------------------------------------------------------
<<<<<<< HEAD
#TOC> 1 Preparations 53 #TOC> 1 Preparations 53
#TOC> 2 Loading a GEO Dataset 84 #TOC> 2 Loading a GEO Dataset 84
#TOC> 3 Column wise analysis - time points 154 #TOC> 3 Column wise analysis - time points 154
@ -46,6 +47,20 @@
#TOC> 5.1 Final task: Gene descriptions 490 #TOC> 5.1 Final task: Gene descriptions 490
#TOC> 6 Improving on Discovery by Differential Expression 495 #TOC> 6 Improving on Discovery by Differential Expression 495
#TOC> 7 Annotation data 577 #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>
#TOC> ========================================================================== #TOC> ==========================================================================
@ -586,6 +601,7 @@ GSE3635annot <- getGEO("GSE3635", GSEMatrix = TRUE, getGPL = TRUE)
GSE3635annot <- GSE3635annot[[1]] GSE3635annot <- GSE3635annot[[1]]
# ... and the feature data is then available in the GSE3635@featureData@data # ... and the feature data is then available in the GSE3635@featureData@data
<<<<<<< HEAD
# slot: # slot:
str(GSE3635annot@featureData@data) str(GSE3635annot@featureData@data)
GSE3635annot@featureData@data[ 1:20 , ] 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: # 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" GSE3635@annotation # "GPL1914"
# ... and downloaded it directly from NCBI: # ... and downloaded it directly from NCBI:
@ -617,9 +640,13 @@ GPL1914 <- getGEO("GPL1914")
str(GPL1914) str(GPL1914)
# ... from which we can get the data - which is however NOT necessarily # ... 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 # 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 # of data elements are factors and will likely have to be converted before
# use. # use.
=======
# matched to the rows of our expression dataset.
>>>>>>> b17a9e202ad3429a716683538b3d0ed8d7d9ff9e
# [END] # [END]