Finding IQR String Groups
I want to find the IQR of a range of values in a data frame. These values are grouped as well, so I need to find the IQR of each group in the dataframe. I have the following table:
Block DNAname Spot_Size Molarity Cy3_Fluorescence
1 DNA 01 100pl 100 14266
1 DNA 01 100pl 100 16020
1 DNA 01 100pl 100 15705
1 DNA 01 100pl 100 15783
1 DNA 01 100pl 100 15834
1 DNA 01 100pl 50 12248
1 DNA 01 100pl 50 12209
1 DNA 01 100pl 50 12511
1 DNA 01 100pl 50 12316
1 DNA 01 100pl 50 12469
1 DNA 01 100pl 25 9626
1 DNA 01 100pl 25 9804
1 DNA 01 100pl 25 9794
1 DNA 01 100pl 25 10020
1 DNA 01 100pl 25 9739
1 DNA 01 100pl 10 7158
1 DNA 01 100pl 10 6802
1 DNA 01 100pl 10 7378
1 DNA 01 100pl 10 5949
1 DNA 01 100pl 10 7484
1 DNA 01 100pl 5 5257
1 DNA 01 100pl 5 5560
1 DNA 01 100pl 5 6076
1 DNA 01 100pl 5 5925
I am running the following code to find the IQR:
aggregate(Cy3.DNA1.100pl.1uM$Cy3_Fluorescence, list(Molarity=
Cy3.DNA1.100pl.1uM$Molarity, Spot_Size=Cy3.DNA1.100pl.1uM$Spot_Size ), IQR)
This gives me an output:
Molarity Spot_Size x
5 100pl 384
10 100pl 576
25 100pl 65
50 100pl 221
100 100pl 129
This conclusion correctly groups all molarities, but the IQR is incorrect. If the above code has a value as a function instead of an IQR, the value for x (function value) is correct:
Molarity Spot_Size x
5 100pl 5752.4
10 100pl 6954.2
25 100pl 9796.6
50 100pl 12350.6
100 100pl 15521.6
The expected IQRS should be as follows:
Molarity IQR
100 324.25
50 258
25 363
10 519.5
5 400
Any help would be much appreciated. If anyone has any ideas how I might perform this function for IQR when there are groups of spot sizes (where spot sizes range from 100pl-400pl) including molarity categories, I would love to hear them.
Thank you for that.
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It is not clear if your problem is related to aggregation or your (??) IQR definition. There are many ways to calculate IQR (see this and this ). As far as I can tell, none of these give results in your post.
When it comes to aggregation based on spot size and molarity, there are two ways:
# use aggregate(...) in base R - will be slow with large datasets
aggregate(Cy3_Fluorescence~Molarity+Spot_Size,df,IQR)
# Molarity Spot_Size Cy3_Fluorescence
# 1 5 100pl 478.5
# 2 10 100pl 576.0
# 3 25 100pl 65.0
# 4 50 100pl 221.0
# 5 100 100pl 129.0
# use data.table - will be extremely fast.
library(data.table)
setDT(df)[,list(IQR=IQR(Cy3_Fluorescence)),by=list(Molarity,Spot_Size)]
# Molarity Spot_Size IQR
# 1: 100 100pl 129.0
# 2: 50 100pl 221.0
# 3: 25 100pl 65.0
# 4: 10 100pl 576.0
# 5: 5 100pl 478.5
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