Re: [R] Mann-Whitney by group

[Oxenstierna]

lapply(thing, function(x) x[['p.value']]) --works very well, thank you.

Not to be a chore, but I'm interested in comparing the results of
wilcox.test--and the methodology we've employed so far--with the results and
methodology of wilcox_test (library("coin")).  So, I'd like to compare
groups 5 and 6 across A through H using wilcox_test, and then I'd like to
extract the p-values.  Going through the same methodology as above, but
replacing wilcox.test with wilcox_test has failed, and so has the p.value
extraction method:  lapply(thing, function(x) x[['p.value']]) .

I believe the latter failure has to do with the fact that the coin package
has a built-in class and built-in extraction method (pvalue() to extract and
class "IndependenceTest"), but I don't know how to work around it.  For
example, for a single comparison:  wilcox_test(A~Group, Dtb) works fine, and
pvalue(wilcox.test(A~Group, Dtb)) extracts the p-value.

So, any ideas about how to compare groups 5 and 6 across A through H using
wilcox_test?

Many thanks!


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Re: [R] Mann-Whitney by group

[Oxenstierna]

This works very well--thanks so much.

By way of extension:  how would one extract elements from the result object?

For example:

thing<=apply(Dtb[,3:10], 2, function(x) wilcox.test(x~Dtb$Group))

summary(thing)$p.value

Does not provide a list of p-values as it would in a regression object. 
Ideally, I would like to be able to extract the W score and p-value by
A,B,C,...

Any ideas greatly appreciated!


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Re: [R] Mann-Whitney by group

[Oxenstierna]

Hi David,

Thank you for the insight:  I could have sworn I added a picture of the
data, but providing the actual data is worlds easier to deal with, I'm sure. 
I've never used dput(), so I entered it using the dataframe in question as
the object, and I've pasted the results below.

Essentially, I would like to run the two-sample independent test, comparing
Group 5 (CD8.14 through CD8.17) to Group 6 (CD8.18 through CD8.21). So, for
A, test Group 5 agains Group 6, for B, test Group 5 against Group 6, and so
on.  I'm not going to muddy the waters by telling you what I've tried;
suffice it to say that I'm looking for insights into how to structure R
commands to compare groups of data of this format.

Many thanks in advance,

David


structure(list(Gene = structure(c(1L, 12L, 19L, 20L, 21L, 22L, 
23L, 24L, 25L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 13L, 
14L, 15L, 16L, 17L, 18L), .Label = c("CD8.1", "CD8.10", "CD8.11", 
"CD8.12", "CD8.13", "CD8.14", "CD8.15", "CD8.16", "CD8.17", "CD8.18", 
"CD8.19", "CD8.2", "CD8.20", "CD8.21", "CD8.22", "CD8.23", "CD8.24", 
"CD8.25", "CD8.3", "CD8.4", "CD8.5", "CD8.6", "CD8.7", "CD8.8", 
"CD8.9"), class = "factor"), Group = structure(c(8L, 8L, 8L, 
9L, 9L, 9L, 10L, 10L, 10L, 11L, 11L, 11L, 11L, 12L, 12L, 12L, 
12L, 13L, 13L, 13L, 13L, 14L, 14L, 14L, 14L), .Label = c("Fabbf Ova CD40", 
"Fabbf Ova MHC2", "Fabbf Ova WT", "Fabbf WT", "Naïve CD40", "Naïve MHC II", 
"Naïve WT", "1", "2", "3", "4", "5", "6", "7"), class = "factor"), 
A = c(19.4701946749544, 0.679440926463348, 0.69035683372563, 
0.347105466158261, 0.435480792190284, 0.338699910286907, 
0.651378057031152, 0.707065053752258, 0.685244609506316, 
0.816673858871597, 0.597009097584509, 0.592331304482431, 
0.709359033358704, 0.628406759227531, 0.78158729467231, 1.0422377526669, 
0.61560003251142, 0.463755016733183, 0.419700860701392,
0.380946898502731, 
0.41156961153081, 0.471790683365624, 0.552773224145722,
0.466787799928649, 
0.767624372542755), B = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), C = c(0.914649979331863, 
1.443086801592, 0.928280641141244, 0.467498974059775, 0.668742025741347, 
0.568417298005388, 0.778907650835673, 0.778765181169635, 
1.01103488277517, 0.674133483128923, 0.830400022230133,
0.652687178870627, 
0.746893950266518, 0.765498308522646, 1.01273201749333,
1.00309616129672, 
0.63015975419947, 0.615905247119739, 0.615687625199691,
0.503136087800137, 
0.566164026974035, 0.631519467967541, 0.822126705285366, 
0.543873075815645, 1.00596108625425), D = c(13.3272657341526, 
3.08914950309865, 1.71836820240434, 0.723301573710509, 1.21014411624732, 
1.92899377364865, 1.80280408189187, 2.25057819266424, 2.23876060313374, 
1.30849425313072, 1.58782967140617, 1.19199809794126, 1.64151140806787, 
0.241017500596534, 0.364896032519483, 0.322953808735804, 
0.2052110581509, 0.927601295331376, 0.808910781520832,
0.538033121081646, 
0.655348783504307, 0.564449549672088, 0.521729926793001, 
0.414305517285192, 0.507084483980948), E = c(56.2830291897158, 
9.76091939190267, 4.80922410182105, 17.0056576949022, 20.851046177766, 
17.9057247086369, 5.93332779160845, 4.73058157592946, 5.59155211460608, 
9.67484467290805, 5.92374864612388, 7.12393623733123, 5.33576126730867, 
10.3943422629275, 10.8732527705049, 12.4861085370674, 12.0918705721064, 
13.3210661695018, 10.9410344557684, 15.1298307761675, 13.0708078246191, 
9.4445293976312, 6.94340249514349, 5.07888688780375, 8.33846787814466
), F = c(15.0459568981729, 21.6362955612539, 9.66673955488981, 
27.2276698483913, 18.1090094072926, 20.0952712980862, 24.9249499974856, 
23.5540183530194, 29.6638363657906, 28.9779309040733, 42.0402820641407, 
33.8068160394092, 51.7299064374737, 37.8306751403421, 43.1955470199259, 
45.5125262939585, 40.3109474523637, 23.6341894633273, 23.9721353180788, 
20.4920649252818, 24.8898447627354, 34.2686409607416, 31.3815198841165, 
31.4947528368753, 43.2686436885025), G = c(15.9703031418086, 
5.30495997585743, 3.07594974529074, 8.28703732907722, 10.9437825143868, 
6.91196232523896, 2.97808148581742, 2.6386825521864, 2.2415006913088, 
5.00747306438661, 2.65238188782831, 3.18277515130905, 3.14638620532385, 
2.5149505923191, 2.48862112414046, 2.97170069886913, 1.91643165326171, 
7.50682774199005, 5.39102206185423, 5.2498453524987, 7.17519969844757, 
2.66448841457179, 2.78444235996995, 1.62286520735228, 2.48760726398266
), H = c(-1, -1, -1, 0.0036561124481055, 0.010723007432761, 
0.0196616746380801, 0.0371046164124276, -1, 3.27378673314144e-05, 
-1, -1, -1, -1, 0.00816215783906802, 21.5424904701651, 9.57900616157724, 
0.00735942043489242, 1.50346040901698, 0.0909450037365435, 
1.49237001404701e-05, 0.000775741472561218, -1, 17.9023582944659, 
0.0176891314806093, 33.4326253626981)), .Names = c("Gene", 
"Group", "A", "B", "C", "D", 

Re: [R] Help! Please recommend good books/resources on visualizing data and understanding multivariate relations...

[Oxenstierna]

I'm a fan of Ggobi--which works well with or without R--but I'm not sure how
it handles enormous data sets. I second the Tufte recommendation, and add: 
Interactive and Dynamic Graphics for Data Analysis. 

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