User: grashow

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Posts by grashow

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Comment: C: DESEq2 contrast statement syntax and design statement question
... Thank you for the clarification! We're still searching for a biostatistician to help, but this helps us get closer on our own. ...
written 2.2 years ago by grashow0
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DESEq2 contrast statement syntax and design statement question
... Hi, Thank you for answering our previous questions. We've made progress addressing our shared controls and "model matrix not full rank" issues. As a reminder, we had 8 chemicals (plus control) tested at 4 concentrations both with and without estrogen (E2). We had three biological replicates and thr ...
deseq2 interactions contrast written 2.2 years ago by grashow0 • updated 2.2 years ago by Michael Love26k
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In DESeq2- getting an "hatmatrix %*% t(y)" error signal only after running collapseReplicates
... Hi, We have an experimental design where 8 chemicals plus control were applied at 4 concentrations with and without estrogen (called E2, either a 1 or a 0). We wish to control for lane (i.e. batch, three total). Given this design, the design statement would look like this: design = ~lane + E2 + ch ...
deseq2 collapsereplicates written 2.3 years ago by grashow0 • updated 2.3 years ago by Michael Love26k
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Comment: C: DESeq2- what to do when two conditions share controls?
... Thank you for all of these answers- this makes sense. ...
written 2.4 years ago by grashow0
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Comment: A: DESeq2- what to do when two conditions share controls?
... Hi Michael, Thanks again for all these answers. Here's what I'm confused about- doesn't each of the treated conditions need to refer back to a control condition to establish which genes are differentially expressed? In other words, if I turn each of the "control"-labeled conditions into "Tam" at co ...
written 2.5 years ago by grashow0
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Comment: A: DESeq2- what to do when two conditions share controls?
... Hi Michael, Thanks for your response. To operationalize what you're recommending, would I create a new version of my colData table, where the rows labeled as "control" under the "chemical" column with a Conc_uM = 0.0 be changed to Tam? Will this limit my ability to analyze PFOA data because it won' ...
written 2.5 years ago by grashow0
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Comment: C: DESeq2- what to do when two conditions share controls?
... I have been using the collapseReplicates function in DESeq2 to account for the technical replicates. You are correct about identifying the technical replicates. The problem comes with the way the plates were laid out. If we want to do dose response curves and more, I believe that DESeq2 expects tha ...
written 2.5 years ago by grashow0
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Comment: C: DESeq2- what to do when two conditions share controls?
... Yes, sorry- the "E2" column represents with estrogen as a "1" and those without with a "0". The first letters in the row names ("PL1A", etc) represent plate number, and the later letters ("C08") represent well locations. "Rep" refers to replicates- either 1, 2 or 3. Here is a longer version of that ...
written 2.5 years ago by grashow0
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Comment: A: DESeq2- what to do when two conditions share controls?
... Here is the colData, although it is incorrectly formatted for DESeq2. As currently written, the controls (both treated and untreated with estrogen) are used in the "chemical" column. I believe what I need is for the controls to be represented instead as associated with a chemical at a concentration ...
written 2.5 years ago by grashow0
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DESeq2- what to do when two conditions share controls?
... Hi, I have count data from an experiment where we used 8 chemicals tested at 4 concentrations each, both in the presence of estrogen and without estrogen. There were 3 technical replicates and 3 biological replicates. The DESeqDataSetFromMatrix command looks like this (without interactions): dds & ...
deseq2 written 2.5 years ago by grashow0

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