Dear Pantelis,

at
http://genomics-lab.fleming.gr/fleming/Cereghini/metaseqr_wt_vs_het_run107/index.html
http://genomics-lab.fleming.gr/fleming/Cereghini/metaseqr_wt_vs_mut_run128/index.html
http://genomics-lab.fleming.gr/fleming/Cereghini/metaseqr_wt_vs_mut_run142/index.html
http://genomics-lab.fleming.gr/fleming/Cereghini/metaseqr_wt_vs_tr_run20/index.html
are the meteseqr reports for all Cereghini runs.

At
http://genomics-lab.fleming.gr/fleming/Cereghini/run142/
you'll find the following scatterplots:
WT_vs_HET_r107_VS_WT_vs_HET_r142.png
WT_vs_HET_r107_VS_WT_vs_MUT_r128.png
WT_vs_MUT_r128_VS_WT_vs_HET_r142.png
WT_vs_TR_r20_VS_WT_vs_HET_r107.png
WT_vs_TR_r20_VS_WT_vs_HET_r142.png
WT_vs_TR_r20_VS_WT_vs_MUT_r128.png

Each compares diff.exp in 2 different comparisons.

The groups are:
r20:
SC1_E15.5_1-3
SC2_E15.5_2-4

r107:
SCR10-E145-4wt.bam
SCR12-E145-6Het.bam
SCR13-E145-3wt.bam
SCR14-E145-5Het.bam

r128:
DrSCereghini_4RNAseq_SCR17r-65n5mut-bc4_SCR19r-65n11wt-bc15
DrSCereghini_4RNAseq_SCR16r-65n2mut-bc2_SCR18r-65n8wt-bc5

r142:
DrSCereghini_4RNAseq_SCR20-6wtt-bc5_SCR22-5Het-bc14
DrSCereghini_4RNAseq_SCR21-7wt-bc9_SCR23-8Het-bc15

Correlation between the diff.exp results are:
DE1_vs_DE2                       Pearson Correlation
WT_vs_TR_r20_VS_WT_vs_HET_r107   0.5380191 
WT_vs_TR_r20_VS_WT_vs_HET_r142	 0.3830663 
WT_vs_TR_r20_VS_WT_vs_MUT_r128	 0.9214371 
WT_vs_HET_r107_VS_WT_vs_HET_r142  -0.019153
WT_vs_HET_r107_VS_WT_vs_MUT_r128  0.3954548
WT_vs_MUT_r128_VS_WT_vs_HET_r142 0.5980661 

We'll discuss this...
Martin


WT_r107_VS_WT_r128.png 0.6656025 
WT_r107_VS_WT_r142.png 0.2035694 
WT_r128_VS_WT_r142.png 0.6529015 
WT_r20_VS_WT_r107.png 0.5660856 
WT_r20_VS_WT_r128.png 0.872482 
WT_r20_VS_WT_r142.png 0.6000171 



At
http://genomics-lab.fleming.gr/fleming/Cereghini/metaseqr_e15.5/index.html
http://genomics-lab.fleming.gr/fleming/Cereghini/metaseqr_e14.5/index.html
http://genomics-lab.fleming.gr/fleming/Cereghini/metaseqr_HoxB7cre/index.html
http://genomics-lab.fleming.gr/fleming/Cereghini/metaseqr_RCAD_P1/index.html
are the meteseqr reports for all Cereghini runs.

At
http://genomics-lab.fleming.gr/fleming/Cereghini/run142/
you'll find the following scatterplots with the following
correlations between the significantly differentially expressed genes:

DE1_vs_DE2                                   Pearson Correlation
diff_exp_e15.5_VS_diff_exp_e14.5.png         0.5380191 
diff_exp_e14.5_VS_diff_exp_HoxB7cre.png      0.395454
diff_exp_e14.5_VS_diff_exp_RCAD_P1.png       -0.01915
diff_exp_e15.5_VS_diff_exp_HoxB7cre.png      0.9214371
diff_exp_e15.5_VS_diff_exp_RCAD_P1.png       -0.01915
diff_exp_HoxB7cre_VS_diff_exp_RCAD_P1.png    0.5980661


Also, scatterplots and
correlations between expression values of all genes in the WT samples are:
WT1_vs_WT2                              Pearson Correlation
WT_e15.5_VS_WT_e14.5.png                0.9438614 
WT_e14.5_VS_WT_HoxB7cre.png             0.950614  
WT_e14.5_VS_WT_RCAD_P1.png              0.9339366 
WT_e15.5_VS_WT_HoxB7cre.png             0.9573134 
WT_e15.5_VS_WT_RCAD_P1.png              0.9409653 
WT_HoxB7cre_VS_WT_RCAD_P1.png           0.9498121