Hi,
I've a problem to compute DE analysis with DESeq. I've a data.frame a with 10 samples ( one group of four samples and one group of six samples ).
i
here's the code I used :
After that I've this error :
Indeed, when I look after the sizeFactors :
So I don't understand where is the problem. Here's my data.frame :
Thanks,
N.
P.S.: Simon help me pleeeease
I've a problem to compute DE analysis with DESeq. I've a data.frame a with 10 samples ( one group of four samples and one group of six samples ).
i
here's the code I used :
Code:
cds <- newCountDataSet(a,conditions=c(rep("a",4),rep("b",8))) cds <- estimateSizeFactors(cds) cds <- estimateVarianceFunctions(cds)
Code:
Erreur dans estimateVarianceFunctions(cds) : NAs found in size factors. Have you called already 'estimateSizeFactors'?
Code:
sizeFactors(cds) s1 s2 s3 s4 s5 s6 s7 s8 s9 s10 NA NA NA NA NA NA NA NA NA NA
So I don't understand where is the problem. Here's my data.frame :
Code:
s1 s2 s3 s4 s5 s6 s7 s8 s9 s10 1 12 353 222 0 0 0 0 1 0 804 2 3 131 26 148 2 139 39 0 53 65 3 0 10 1 6 1 10 0 0 22 51 4 0 35 0 12 0 12 0 0 0 0 5 0 0 4 3 0 0 3 0 23 0 6 0 8 3 3 0 2 4 0 1 2 7 0 4 1 7 0 2 1 0 5 1 8 0 4 0 7 0 6 2 0 2 0 9 0 0 0 0 0 0 0 0 15 5 10 0 0 0 0 0 0 0 0 17 0 11 0 6 1 0 1 5 2 0 0 0 12 0 1 0 3 1 2 1 0 5 2 13 0 1 4 3 2 0 2 0 2 0 14 0 2 3 2 0 1 2 0 2 1 15 0 1 1 3 1 0 2 0 4 0 16 0 0 0 0 0 0 0 0 0 12 17 0 0 0 0 0 0 0 0 11 0 18 0 0 0 0 0 0 0 0 11 0 19 0 0 0 0 0 7 3 0 0 0 20 0 0 1 0 0 0 1 0 7 0 21 0 0 0 0 0 0 0 0 9 0 22 0 0 2 0 1 0 0 0 5 0 23 0 0 1 0 1 0 0 0 2 4 24 0 0 0 3 0 0 0 0 2 3 25 0 0 0 0 0 0 0 0 6 2 26 0 0 0 0 0 0 0 0 4 3 27 1 0 0 0 0 1 0 0 3 1 28 0 0 0 0 0 0 0 0 4 2 29 0 0 4 0 1 0 0 0 0 0 30 0 1 0 1 0 0 0 0 3 0 31 0 1 3 0 1 0 0 0 0 0 32 0 0 1 2 0 0 0 0 2 0 33 0 0 0 1 0 2 1 0 1 0 34 0 1 0 0 1 0 0 0 2 0 35 0 0 1 1 0 0 0 0 2 0 36 0 0 1 3 0 0 0 0 0 0 37 0 0 0 2 0 0 0 0 1 1 38 0 0 0 0 0 2 1 0 1 0 39 0 0 0 0 0 0 0 0 4 0 40 1 0 0 0 1 0 0 0 1 0 41 0 2 0 1 0 0 0 0 0 0 42 0 1 1 0 0 0 0 0 1 0 43 0 1 0 0 0 0 1 0 1 0 44 0 1 0 1 0 0 0 0 1 0 45 0 0 2 0 0 1 0 0 0 0 46 0 0 2 0 0 0 0 0 1 0 47 0 0 1 0 0 2 0 0 0 0 48 0 0 2 0 0 0 0 0 0 1 49 0 0 0 0 0 0 0 0 2 1 50 0 0 0 1 0 0 1 0 1 0 51 0 0 0 0 0 0 0 0 2 1 52 0 0 0 0 0 0 0 0 3 0 53 0 0 0 0 0 0 0 0 3 0 54 0 0 0 0 0 0 0 0 3 0 55 0 0 0 0 0 1 1 0 0 0 56 1 0 0 0 0 0 0 0 1 0 57 1 0 0 1 0 0 0 0 0 0 58 0 0 0 1 0 0 0 0 1 0 59 0 1 0 0 0 0 1 0 0 0 60 0 1 0 1 0 0 0 0 0 0 61 0 0 0 0 2 0 0 0 0 0 62 0 1 1 0 0 0 0 0 0 0 63 0 0 1 0 0 1 0 0 0 0 64 0 2 0 0 0 0 0 0 0 0 65 0 0 1 0 0 0 0 0 1 0 66 0 0 1 0 0 0 1 0 0 0 67 0 0 1 1 0 0 0 0 0 0 68 0 0 0 0 0 0 0 0 0 2 69 0 0 0 2 0 0 0 0 0 0 70 0 0 0 1 0 0 0 0 1 0 71 0 0 0 1 0 0 0 0 1 0 72 0 0 0 1 0 0 0 0 1 0 73 0 0 0 1 0 0 0 0 1 0 74 0 0 0 2 0 0 0 0 0 0 75 0 0 0 2 0 0 0 0 0 0 76 0 0 0 0 0 0 0 0 2 0 77 0 0 0 1 0 0 0 0 0 1 78 0 0 0 1 0 0 0 0 1 0 79 0 0 0 0 1 0 0 0 0 1 80 0 0 0 0 1 0 0 0 0 1 81 0 0 0 0 1 0 0 0 0 1 82 0 0 0 0 0 1 0 0 1 0 83 0 0 0 0 0 2 0 0 0 0 84 0 0 0 0 0 1 0 0 1 0 85 0 0 0 0 0 1 0 0 1 0 86 0 0 0 0 0 1 0 0 1 0 87 0 0 0 0 0 0 1 0 1 0 88 0 0 0 0 0 0 2 0 0 0 89 0 0 0 0 0 0 2 0 0 0 90 0 0 0 0 0 0 0 0 2 0 91 0 0 0 0 0 0 0 0 2 0 92 0 0 0 0 0 0 0 0 2 0 93 0 0 0 0 0 0 0 0 2 0 94 0 0 0 0 0 0 0 0 2 0 95 0 0 0 0 0 0 0 0 2 0 96 0 0 0 0 0 0 0 0 2 0 97 0 0 0 0 0 0 0 0 2 0 98 0 0 0 0 0 0 0 0 2 0 99 0 0 0 0 0 0 0 0 2 0 100 0 0 0 0 0 0 0 0 2 0
N.
P.S.: Simon help me pleeeease
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