User: mariannapauletto

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Posts by mariannapauletto

<prev • 14 results • page 1 of 2 • next >
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Comment: C: DE genes and variability between biological replicates: edgeR
... Thank you, sorry for that ...
written 8 months ago by mariannapauletto30
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Comment: A: DE genes and variability between biological replicates: edgeR
... Thank you for your reply. That's clear. Actually, with recent datasets I've implemented exactly the same approach you mentioned (filterByExpr and glmQLF). But: in your opinion, looking at the results obtained with the previous version and the code I used (including filtering by low expression CPM ...
written 8 months ago by mariannapauletto30
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Comment: A: DE genes and variability between biological replicates: edgeR
... Hi ATpoint, thank you for your quick reply. I'm speaking about the results of an analysis conducted in the past with an edgeR version lacking the filterByExpr command. Anyway I filtered data with the approach suggested by the manual of that version (see below) This is the code: >keep < ...
written 8 months ago by mariannapauletto30
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Comment: C: DE genes and variability between biological replicates: edgeR
... sorry I dd a mess with the comments, see the reply below ...
written 8 months ago by mariannapauletto30
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DE genes and variability between biological replicates: edgeR
... Hi guys, I'm dealing with DE genes resulted from edgeR analysis comparing two experimental groups (n=3 per group) I noticed that some DEGs show high variability within replicates... Do you think that the program takes into account this aspect? Are these DEGs reliable or not? If not, how to filter t ...
gene rna-seq written 8 months ago by mariannapauletto30
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Comment: C: Deseq2 with one factor and multiple levels
... Hi Kevin, I did the analysis as you suggested. I noticed that the log2fold changes are REALLY different if using `lfcShrink`. For example for the most DE gene I got a log2FC of 4 and 0.05 using lfcShrink and results, respectively. Do you expect such a big difference?? Best Marianna ...
written 13 months ago by mariannapauletto30
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Comment: C: Deseq2 with one factor and multiple levels
... Thank you Kevin, really appreciated Marianna ...
written 13 months ago by mariannapauletto30
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Comment: C: Deseq2 with one factor and multiple levels
... Hi Kevin, thank you for your reply! If I use `~ condition`, then the first level of the factor "condition" is fixed as a control/base condition and all the other levels will be compared to this control condition. How to deal with that?? I thought the only solution was to remove the intercept, so ...
written 13 months ago by mariannapauletto30
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Deseq2 with one factor and multiple levels
... Dear all, I'm dealing with and RNA-seq experiment with a total of 11 different conditions. I'd like to do pairwise comparisons between some of them (without having a fixed base/ctrl condition). To do that, I'm planning to use the Wald-test. After setting conditions (n=11), this is the command I ...
deseq2 rna-seq written 13 months ago by mariannapauletto30 • updated 13 months ago by Kevin Blighe65k
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Comment: C: batch effect Deseq2 Wald test
... Thank you Devon Ryan ...
written 19 months ago by mariannapauletto30

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