Judith.A.Hoyland CD24+/- microarray, 2018

(Affy microarray)

(n=7)







Order: By time (wks) By pos neg, and then by time
Scales: linear log log+1



e.g. SOX9, T, TGFB1


Samples
M708_pos_8wk.CEL
M728_pos_7.5wk.CEL
M729_pos_12wk.CEL
M739_neg_14wk.CEL
M739_pos_14wk.CEL
M753_neg_8.5wk.CEL
M753_pos_8.5wk.CEL

Normalistation and expression analysis
Done with Partek GS 6.6 using RMA algorithm

PCA
Partek GS

Differential expression pvalues with limma in R
FDR Qvalues calculated with QVALUE
Contrasts:
A - 5 positive versus 2 negative samples
B - 2 positive (M739 and M753) versus 2 negative paired samples (M739 and M753)
C - gene expression change between the 5 positive samples (they represent 5 different developmental stages, 
	so I'm interested in changes with development. 
	
	The order of the samples is: 1st: M728 (7.5 weeks), 2nd: M708 (8 weeks), 3rd: M753 (8.5 weeks), 
	4th: M729 (12 weeks), 5th M739 (14 weeks). 
	
	As such, I am not sure (and probably won't be before we see the data) whether to pair the first 3 
	and compare with the last 2, or whether to compare between the 5 individual samples.
X_vs_Y where 
X = M728Pos, M708Pos and M753 pos
Y =  M729pos and M739pos








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