Hello everybody!
I'm trying to analyse some pyrosequencing data that some colleges sent me. I could get all experiment replicas for each experimental condition. The problem is that for the different genes I can have a different number of replicas. Even more, in some cases some results are missing. I think i should refill those values with 0's or N/A. what should i do in those cases that i do not have value? Working with averages do not provides good statistics
example of data
HEK293-Nach A2 64.09 - 62.06 64.2 -
HEK293-Nach B2 69.97 - 69.3 71.36 -
HEK293-Nach B2 62.22 - 62.26 61.89 -
HEK293-Nach B3 71.59 - 71.64 68.18 -
HEK293-Nach B3 57.61 - 59.55 60.71 -
HEK293-Nach B4 58.39 - 60.47 58.35 -
HEK293-Nach B4 66.21 - 65.46 66.13 -
HEK293-Nach B5 54.93 - 57.03 57.47 -
HEK293-Nach B5 61.58 - 66.07 65.93 -
HEK293-Nach B6 50 - 56.69 55.01 -
HEK293-Nach B6 58.57 - 65.68 63.94 -
HEK293 K 45.1 46.4 42.15 1.9 41.37
HEK293 K 45.92 44.88 42.2 1.74 41.16
HEK293 K 62.49 67.06 59.34 2.35 58.34
HEK293 K 59.21 67.21 58.54 3.75 56.7
What do those numbers in your post mean? Also, why do you have different numbers of replicates for different genes? In a genome-wide (presumably transcriptomic) experiment, you should be getting one count per gene in each sample, so you should have the same number of samples for all genes. On a related note, what do you mean by missing observations? Simply having a count of zero isn't a case of missingness, it just means that expression is probably very low.
the number of my post are measurements for different conditions. I do not know why there are missing values, i did not do the experiment, it was done by some collegues and they sent me it to analyse. That why i think they suggested to analyse it using the average for each condition.
could i do it some how?
p