Question: Problem with p-values calculated by eBayes--corrected format

0

Chen, Zhuoxun •

**40**wrote:Hi Bioconductors,
I am really sorry about sending this email again. I didn't know that
the table on my email will be lost and reformat. I corrected the
format now. Thank you for your patience.
?
I have a very weird problem with the statistics with my microarray
data. I would like to ask for your help.
I am running a microarray with 16 groups, 3 samples/group. On my
genechip, every probe is spotted 2 times.
By comparing two groups (let?s say A and B), I came across a gene that
is very significant by running the following codes, with a p-value=
0.001669417
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--------------------------------------
corfit <- duplicateCorrelation(Gvsn, design = design, ndups = 2,
spacing = 1)
fit <- ?lmFit(Gvsn, design = design, ndups = 2, spacing = 1,
correlation = corfit$consensus)
contrast.matrix <- makeContrasts(A-B, levels=design)
fit2 <- contrasts.fit(fit, contrast.matrix)
fit3 <- eBayes(fit2)
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--------------------------------------
Then, I looked at the raw data; copy and paste onto Excel and did a
simple t-test
?
A B
1 6.938162 7.093199
2 7.012382 8.05612
3 7.000305 6.999078
Avg 6.983616 7.382799
contrast 0.399182
p-value
one tailed, unequal variance, t-test=0.179333
one tailed, equal variance, t-test=0.151844 ?
?
The p-value is NOT even close to 0.05. Then I looked at the contrast
of fit3$coefficient, it is 0.399182, which indicates the data input
for the codes are correct.
I don?t understand why it has such a huge difference on p-value
between those two methods. Could somebody please help me with it?
Thanks,
Zhuoxun Chen
??
SessionInfo:
----------------------------------------------------------------------
---------------------------------------------------------------
R version 2.8.0 (2008-10-20)
i386-pc-mingw32
?locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
?attached base packages:
?[1] grid????? splines?? tools???? stats???? graphics? grDevices
utils???? datasets? methods?? base????
?other attached packages:
?[1] gplots_2.6.0????????? gdata_2.4.2?????????? gtools_2.5.0?????????
org.Hs.eg.db_2.2.6??? GSEABase_1.4.0??????
?[6] PGSEA_1.10.0????????? Ruuid_1.20.0????????? Rgraphviz_1.20.2?????
XML_1.94-0.1????????? bioDist_1.14.0??????
[11] GOstats_2.8.0???????? Category_2.8.0??????? genefilter_1.22.0????
survival_2.34-1?????? RBGL_1.18.0?????????
[16] annotate_1.20.0?????? xtable_1.5-4????????? graph_1.20.0?????????
eArrayCanary.db_1.0.0 annaffy_1.14.0??????
[21] KEGG.db_2.2.5???????? GO.db_2.2.5?????????? RSQLite_0.7-1????????
DBI_0.2-4???????????? AnnotationDbi_1.4.0?
[26] statmod_1.3.6???????? RODBC_1.2-3?????????? RColorBrewer_1.0-2???
vsn_3.8.0???????????? affy_1.20.0?????????
[31] Biobase_2.2.0???????? lattice_0.17-15?????? limma_2.16.3????????
?loaded via a namespace (and not attached):
[1] affyio_1.10.1??????? cluster_1.11.11????? preprocessCore_1.4.0
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--------------------------------------------------------------
?

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modified 10.5 years ago
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Kasper Daniel Hansen ♦

**6.4k**• written 10.5 years ago by Chen, Zhuoxun •**40**