Question: DEseq matrix preparation
0
gravatar for Learner
3.9 years ago by
Learner 200
Learner 200 wrote:

I recently had a question related to having data as integer for DEseq .

One data looks like this will have no problem

> head(df)
  treat treat1 treat2 ctrl ctrl1 ctrl2
1    95     91     88   67    65    84
2    83     97     90   88    85    89
3    99    103     99   73    83    82
4    82     99     94   82    62    72
5    88     90     96   87    61    86
6    92    101     80   74    66    62

but a data like this one will have a problem

head(df2) 
            treat   treat1   treat2  ctrl  ctrl1 ctrl2
    1    0.95    0. 91    0. 88  0. 67   0. 65   0. 84
    2   0. 83    0. 97    0. 90   0.88   0. 85   0. 89
    3    0.99    0.103     0.99  0.73   0. 83    0.82
    4    0.82     0.99    0. 94  0. 82   0. 62    0.72
    5    0.88     0.90    0.96   0.87    0.61    0.86
    6    0.92    0.101     0.80   0.74    0.66    0.62

Do you think if I just normalised the data to above , is OK? is there any other way to do it ?

if I don't do the normalisation, is there any other way ? or any other package ?

deseq R • 842 views
ADD COMMENTlink written 3.9 years ago by Learner 200

The question you need to ask yourself is, "regardless of how I transform my data, is the resulting analysis appropriate?" If the answer to that is, "yes!", then go ahead and "normalize" (transform) the data.

ADD REPLYlink written 3.9 years ago by Devon Ryan94k

@Devon Ryan for sure, but imagine if we make integer the df2, I will get all of them zero. which kind of normalisation would you use ?

ADD REPLYlink written 3.9 years ago by Learner 200

There's no generic answer to that. One first needs to know what the numbers represent. It may not be possible to convert them into a form where using DESeq2 (or equivalent) would be appropriate.

ADD REPLYlink written 3.9 years ago by Devon Ryan94k
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