User: jillian.waters

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Posts by jillian.waters

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Comment: C: DESeq2: different number of significant genes between DESeqDataSetFromMatrix and
... Hi Michael, I ran this, and they are clearly not identical to one another. At first glance the order of the columns is different, as well as some of the values.  After a more thorough look at the input sample information, I can now see that the discrepancy is that in my input sample_table_2 the fi ...
written 17 months ago by jillian.waters0
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DESeq2: different number of significant genes between DESeqDataSetFromMatrix and DESeqDataSetFromHTSeqCount
... Hello, I've been running in to some troubles with my data analysis with DESeq2, and one thing I decided to confirm was whether I was checking the difference in my results when I used an input count table for DESeqDataSetFromMatrix or when I followed the guidelines for DESeqDataSetFromHTSeqCount. In ...
deseq2 deseqdataset deseqdatasetfrommatrix written 17 months ago by jillian.waters0 • updated 17 months ago by Michael Love23k
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Comment: C: DESeq2: error invalid class SummarizedExperiment object when creating DESeqDataS
... I edited the above, as I realize I had created that conda environment early October, and was thinking of a different environment that I created this week. Either way, this was a relatively recent install. Summarized Experiment was not installed directly by me, but would have been one of the dependen ...
written 17 months ago by jillian.waters0
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Comment: C: DESeq2: error invalid class SummarizedExperiment object when creating DESeqDataS
... Dear Martin and Michael, Thank you both so much for the prompt feedback! You are indeed correct: my packages were out of date. There were 28 packages that were old. I updated all of the packages and the issue is now resolved.  I just want to make a note here in case anyone else stumbles upon this ...
written 18 months ago by jillian.waters0
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DESeq2: error invalid class SummarizedExperiment object when creating DESeqDataSetFromMatrix
... Hello, I am trying to create the DESeqDataSetFromMatrix, and am receiving an error that there is an invalid class "summarizedExperiment" object. I initially thought there was something wrong with my input files, but I receive the same errors when I use the Pasilla dataset and enter in all code as o ...
deseq2 written 18 months ago by jillian.waters0 • updated 18 months ago by Michael Love23k

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