Deleted:PCA from gene count matrix with two conditions
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4 months ago
dzisis1986 ▴ 40

I have a count matrix like this :

Gene    1_T1    2_T1    3_T1    1_T2    2_T2    3_T2
ENSG00000223972 69.88   404.93  6757    898.9   6434    664.59
ENSG00000227232 75.72   0   567 685 0   629.94
ENSG00000133226 43  56  532 357.9   0   493.3
ENSG00000187010 834 666 65  0   54,67   323
ENSG00000224129 0   234.9   3234    655 345 312
ENSG00000236810 554 42  4   5   43  98
ENSG00000179163 77  4322    251 565 212 7
ENSG00000232557 88  34  12  2   22  9888
ENSG00000238084 978 0   233 32  123 7789

for 700 samples in two conditions T1 and T2 ( 350 T1 and 350 T2) for a list of 10000 genes. Could you please tell me how i will create a pca plot with two color vectors for T1 and T2 without using Deseq2. I want to check the pca from count reads .

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