Entering edit mode
Chen, Zhuoxun
▴
40
@chen-zhuoxun-3131
Last seen 10.1 years ago
> Hi Bioconductors,
>
>
>
>
> 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
th
> at is very significant by running the following codes, with a p-valu
> e= 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$consensus)
>
> contrast.matrix <- makeContrasts(A-B, levels=design)
>
> fit2 <- contrasts.fit(fit, contrast.matrix)
>
> fit3 <- eBayes(fit2)
>
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---------------------------------------------------------------------
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>
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> Then, I looked at the raw data; copy and paste onto Excel and did a
> simple t-test
>
>
>
>
>
> A
>
> B
>
> 1
>
> 6.938162
>
> 7.093199
>
> 2
>
> 7.012382
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> 8.05612
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> 3
>
> 7.000305
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> 6.999078
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>
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>
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>
> Avg
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> 6.983616
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> 7.382799
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> contrast
>
> 0.399182
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> p-value
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> one tailed, unequal variance, t-test
>
> 0.179333
>
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> one tailed, equal variance, t-test
>
> 0.151844
>
>
>
> The p-value is NOT even close to 0.05. Then I looked at the contrast
> of fit3$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
betw
> een those two methods. Could somebody please help me with it?
>
>
>
> Thanks,
>
> Zhuoxun Chen
>
>
>
>
>
> SessionInfo:
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----------------------------------------------------------------------
>
> 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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