How to insert a qvalues column in a dataframe with pvalues in R
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@953c4872
Last seen 3 months ago
Mexico

Hi. I have a dataframe containing information about 15923 genes. This dataframe when run includes the genes as rows, and 3 columns, one of those is pvalues. I extracted those pvalues and calculated further q values in another variable(which is numeric class). Now, I want to enter this new column with q values in my original dataframe without qvalues. What can I do? Any advice would be welcome. Here's the code

 pvales
                statistic            dm      p.value
1367452_at    -1.84814800 -0.0562176498 1.140826e-01
1367453_at    -2.71097079 -0.0802710103 3.506081e-02
1367454_at    -0.92826551 -0.0257576988 3.890868e-01
1367455_at     0.70750680  0.0400606878 5.057901e-01
1367456_at     0.84743580  0.0593943620 4.292541e-01
1367457_at    -0.37692044 -0.0216194781 7.192035e-01
1367458_at    -1.75960025 -0.0970041731 1.289665e-01
1367459_at    -3.66411656 -0.0581113209 1.052771e-02
1367460_at     1.49730259  0.1177830175 1.849593e-01
1367461_at    -2.03376701 -0.0633097763 8.820243e-02
1367462_at     3.42504248  0.2544636982 1.405643e-02
1367463_at     4.13685795  0.1472356112 6.100013e-03
1367464_at    -2.32400280 -0.1560921723 5.912406e-02
1367465_at     3.30317292  0.1039470997 1.634312e-02
1367466_at    -0.89825589 -0.0279229387 4.036530e-01

I want to add an extra column of qvalues for each pvalue shown

qvalues dataframe • 167 views
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Entering edit mode
@gordon-smyth
Last seen 6 minutes ago
WEHI, Melbourne, Australia

Here and in a previous post, it seems you're not using recommended Bioconductor workflows for Affymetrix microarrays. If you used a standard workflow then the results data.frame would have gene names and adjusted p-values already added for you. See for example

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