User: Davide

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Davide10
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Posts by Davide

<prev • 14 results • page 1 of 2 • next >
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Comment: C: DE analysis with limma (What to include in the model?)
... I agree on the points Kevin is making. What are the DEG after using "adjusted p-values" for both sets ? ...
written 4 days ago by Davide10
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Comment: C: DE analysis with limma (What to include in the model?)
... Why dont you create a single R script that you feed one file, compare the results using the complete set and another file containing the subset. You can use the same code eg: `design <- model.matrix(~ 0 + group, data)` `contrast <- makeContrasts(A.vs.D = A-D)` That would provide you some c ...
written 4 days ago by Davide10
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Comment: C: DE analysis with limma (What to include in the model?)
... Thats hard to believe that by subsetting the data by columns to just the samples you are testing will differ in DEG from 6000 vs 900 is OK with folks here. My guess is 6000 DEG is the correct one and you messed up somewhere on the second Limma run. ...
written 4 days ago by Davide10
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Comment: C: Unequal group size
... Thanks h.mon for the links. It looks like a Welch's t-test or a Mann.Whitney (assuming the sample size is not too small) is the way to go here. Thanks again ...
written 5 days ago by Davide10
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Comment: C: Unequal group size
... Hypothetically speaking could be height, weight, white blood cell counts etc. If the group size was 10 females versus 5 males would that invalidate a t-test or a wilcoxin test for example ? How would you address the difference in group size assuming it was a problem? Thanks for your help in advanc ...
written 5 days ago by Davide10
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Unequal group size
... Can you compare 5 males in one group versus 10 females in another group by either a t-test or a wilcoxin test ? I heard that the group size difference would be a problem. If you can't then is there a way to test them in a way that accounts for the difference in sample group size. Thank you in adv ...
statistics written 5 days ago by Davide10
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Comment: C: Limma:Coefficients not estimable, please help
... sorry about that RamsRS ...
written 8 days ago by Davide10
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Limma: Coefficients not estimable
... Can someone help with making this design full rank and thereby fix this error: Coefficients not estimable: GroupPlacebo GenderMale Does anyone know how to fix this so I can run as contrasts: cont.matrix = makeContrasts( ana1=GroupGroup1-GroupPlacebo, ana2=(GroupGroup1-Gende ...
R limma rna-seq written 10 days ago by Davide10 • updated 8 days ago by h.mon30k
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Comment: C: check deseq2 design please
... Thanks Asaf Just to clarify, so the following design DESeqDataSetFromMatrix(countData =a,b,design=~ Age + Gender + condition) would give me the differential genes that has the effects of gender and age removed using this code: res<-results(dds, contrast=list("condition_CONTROL_vs_CA ...
written 9 months ago by Davide10 • updated 9 months ago by RamRS28k
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Comment: C: check deseq2 design please
... Thanks Kevin I made the correction to my code. When I run PCA on the normalized counts then Gender appeared to separate the data of controls + cases. Just to clarify, would the following give results that already takes care of the gender and age based on the design DESeqDataSetFromMatrix(cou ...
written 9 months ago by Davide10 • updated 9 months ago by RamRS28k

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