As I was interested in obtaining the normalized data (of my input RNA-Seq count data), I used the .txt file that is present in the Processed_Data folder that is generated after running CLUST. However, (at least for some - I have not checked many) genes, the normalized values do not make sense (the 101 31 4 normalization was used). I give an example here with the input and processed values for gene AT1G52000 in my 18 samples.
For gene AT1G52000, I do not understand why the values for example in sample treatment_Col A/B/C get a minus value while their number of counts are larger in the input data. Maybe I am missing something here.
| CT_Col_A | CT_Col_B | CT_Col_C | CT_OE34_A | CT_OE34_B | CT_OE34_C | CT_KO_A | CT_KO_B | CT_KO_C | treatment_Col_A | treatment_Col_B | treatment_Col_C | treatment_OE34_A | treatment_OE34_B | treatment_OE34_C | treatment_KO_A | treatment_KO_B | treatment_KO_C
As I was interested in obtaining the normalized data (of my input RNA-Seq count data), I used the .txt file that is present in the Processed_Data folder that is generated after running CLUST. However, (at least for some - I have not checked many) genes, the normalized values do not make sense (the 101 31 4 normalization was used). I give an example here with the input and processed values for gene AT1G52000 in my 18 samples.
For gene AT1G52000, I do not understand why the values for example in sample treatment_Col A/B/C get a minus value while their number of counts are larger in the input data. Maybe I am missing something here. | CT_Col_A | CT_Col_B | CT_Col_C | CT_OE34_A | CT_OE34_B | CT_OE34_C | CT_KO_A | CT_KO_B | CT_KO_C | treatment_Col_A | treatment_Col_B | treatment_Col_C | treatment_OE34_A | treatment_OE34_B | treatment_OE34_C | treatment_KO_A | treatment_KO_B | treatment_KO_C
My input data AT1G52000 | 2894.15 | 2083.09 | 2252.74 | 2264.05 | 2326.51 | 2177.02 | 3417.66 | 3123.52 | 3042.18 | 6034.85 | 6116.73 | 6675.45 | 4809.43 | 3728.87 | 3930.98 | 8258.78 | 7762.17 | 7665.90
Processed.txt (normalized data from clust - Processed data file) AT1G52000 | 0.68 | 0.54 | 0.39 | 0.21 | 0.39 | 0.21 | 1.34 | 1.51 | 0.96 | -1.93 | -0.27 | -1.15 | -1.15 | -1.00 | -1.86 | 0.08 | 0.96 | 0.08