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List: bioconductor
Subject: Re: [BioC] DESeq analysis
From: Wolfgang Huber <whuber () embl ! de>
Date: 2012-06-27 17:36:13
Message-ID: 4FEB448D.1020105 () embl ! de
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Dear Narges
thank you for the feedback. Your second question is easy: use the idiom
res1 <- subset(res, padj<0.1)
instead, this will avoid the creation of rows full of NA whenever
res$padj is NA. Alternatively
res[order(res$padj)[1:n], ]
with 'n' your favourite lucky number might be useful. Have a look at the
R-intro manual for more on subsetting of arrays and dataframes in R.
Your first question: can you show us the data for the genes where you
know that they are differentially expressed? Perhaps then it might
become more apparent why DESeq / nbinomtest did not agree. Also, what
does the dispersion plot for cds look like? (This is the plot produced
by plotDispEsts in the vignette).
Best wishes
Wolfgang
narges [guest] scripsit 06/26/2012 06:17 PM:
>
> Hi all
>
> I am doing some RNA seq analysis with DESeq. I have applied the nbinomTest to my \
> dataset which I know have many differentially expressed genes but the first problem \
> is that the result values for "padj"column is almost NA and sometimes 1. and when I \
> want to have a splice from my fata frame the result is not meaningful for me.
> -- output of sessionInfo():
>
> res <- nbinomTest(cds, "Male", "Female")
>
> > head(res)
> id baseMean baseMeanA baseMeanB foldChange log2FoldChange
> 1 ENSG00000000003 0.1130534 0.000000 0.2261067 Inf Inf
> 2 ENSG00000000005 0.0000000 0.000000 0.0000000 NaN NaN
> 3 ENSG00000000419 14.3767155 17.162610 11.5908205 0.6753530 -0.5662863
> 4 ENSG00000000457 17.0174761 15.342800 18.6921526 1.2183013 0.2848710
> 5 ENSG00000000460 3.9414822 2.855099 5.0278659 1.7610131 0.8164056
> 6 ENSG00000000938 16.0894945 18.350117 13.8288718 0.7536122 -0.4081058
> pval padj
> 1 0.9959638 1
> 2 NA NA
> 3 0.3208560 1
> 4 0.5942512 1
> 5 0.4840607 1
> 6 0.5409953 1
>
>
> > res1 <- res[res$padj<0.1,]
> > head(res1)
> id baseMean baseMeanA baseMeanB foldChange log2FoldChange pval padj
> NA <NA> NA NA NA NA NA NA NA
> NA.1 <NA> NA NA NA NA NA NA NA
> NA.2 <NA> NA NA NA NA NA NA NA
> NA.3 <NA> NA NA NA NA NA NA NA
> NA.4 <NA> NA NA NA NA NA NA NA
> NA.5 <NA> NA NA NA NA NA NA NA
>
> my first question is that why although I know there are some differentially \
> expressed genes in the my data, all the padj values are NA or 1 and the second \
> question is this "NA.1" , "NA.2", ..... which are emerged as the first column of \
> object "res1"instead of name of genes
> Thank you so much
> Regards
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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--
Best wishes
Wolfgang
Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber
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