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Question: Pre-filtering DESeqDataSetFromMatrix input
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gravatar for rbronste
8 months ago by
rbronste60
rbronste60 wrote:

A little confused about this, wanted too filter out lines in the matrix with read counts lower than 10 to speed up DESeq2 processing using the following:

dds <- dds[ rowSums(counts(dds)) > 10, ]

However just as before the filtering, after the filtering countData looks like this:

head(countData)
  MBV1 MBV2 MBV3 FBV1 FBV2 FBV3 MBE7 MBE8 MBE9 FBE1 FBE2 FBE3
1    1    1    1    1    1    1    1   66    1    1   50   34
2   11    1    1    1    1    1    6   98    1   11  100    1
3    1    1    1    1    1    1    1    1    1  116  108    1
4    1    1   22    2   84    1    1    4    1   64    1   40
5    1    1   18   74   74    1  102    1  126   22    1    1
6    1    1    1    1   44    1    1    1  122    1    1    1

Wondering where I am going wrong? Thank you.

ADD COMMENTlink modified 8 months ago by James W. MacDonald46k • written 8 months ago by rbronste60
1
gravatar for James W. MacDonald
8 months ago by
United States
James W. MacDonald46k wrote:

Check your parentheses. You are filtering on the rowSums of the matrix, not the number of samples with counts > 10.

ADD COMMENTlink written 8 months ago by James W. MacDonald46k

Thank you! Stupid mistake on my part for sure...

ADD REPLYlink written 8 months ago by rbronste60
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