Question: edgeR, data processing with some missed values
0
gravatar for Pau Marc Muñoz Torres
4.2 years ago by
Barcelona
Pau Marc Muñoz Torres20 wrote:

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

edger data analysis • 499 views
ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by Pau Marc Muñoz Torres20

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.

ADD REPLYlink written 4.2 years ago by Aaron Lun24k

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

ADD REPLYlink written 4.2 years ago by Pau Marc Muñoz Torres20
Answer: edgeR, data processing with some missed values
2
gravatar for Gordon Smyth
4.2 years ago by
Gordon Smyth38k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth38k wrote:

I don't think your colleagues have given you enough information to allow you to analyze this data.

To do a sensible analysis, you need to know in detail what the data values represent. edgeR analyzes counts, not continuous measurements as these seem to be.

You also need to know exactly why there are missing values. Otherwise you can't judge what is the right way to handle them.

ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by Gordon Smyth38k
Answer: edgeR, data processing with some missed values
0
gravatar for Pau Marc Muñoz Torres
4.2 years ago by
Barcelona
Pau Marc Muñoz Torres20 wrote:

ok thanks you. i will ask them for more information

 

thanks

 

ADD COMMENTlink written 4.2 years ago by Pau Marc Muñoz Torres20
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