constructing a DESeqDataSet
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linouhao ▴ 20
@linouhao-15901
Last seen 19 months ago
United States

2017xmq

19 分钟前

the function DESeqDataSetFromMatrix can be used if you already have a matrix of read counts prepared from another source; If you have transcript quantification files, as produced by Salmon, Sailfish, or kallisto, you would use DESeqDataSetFromTximport.

but i always see DESeqDataSetFromMatrix is the most used in tutorial, what is the detailed difference? thanks in advance

deseq2 DESeqDataSet • 1.1k views
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As far as I understood, DESeqDataSetFromTximport has the same purpose that DESeqDataSetFromMatrix but it can directly accept the output of a psedoaligner such as Salmon, producing directly the count matrix.

With DESeqDataSetFromMatrix, you need to have a count matrix already prepared with genes as rows ans samples as columns.

Hope this help

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@mikelove
Last seen 1 day ago
United States

Please see the help files for these functions:

?DESeqDataSet

The help files are where we put details about functions.

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