User: Lila M
Lila M • 350
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- 2 days, 5 hours ago
- Joined:
- 1 year, 11 months ago
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Posts by Lila M
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... Thank you very much for this extensive explanation! ...
written 6 days ago by
Lila M • 350
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... Hi guys, I have a super big data frame (`tbl`) that looks like this:
Sample Chromosome Start End Segment_Mean
1 1 8029121 8164570 0.8332
1 1 8658852 8890987 0.5415
2 1 11846011 12247090 0.5728
2 ...
written 9 days ago by
Lila M • 350
• updated
8 days ago by
Kevin Blighe • 1.2k
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... Many thanks, more clear now :).
So the p-value is of course the only parameter that I have to look in order to accept that at least one of the condition has an effect on exon usage. However the log2fold change give us the information in terms of differential expressed exon in two different condit ...
written 12 days ago by
Lila M • 350
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... Thank you but this not answer my question at all. Anyway the command line that I used:
dsd = estimateSizeFactors(dsd)
dsd = estimateDispersions(dsd)
dsd = plotDispEsts(dsd)
dsd = testForDEU(dsd)
dsd = estimateExonFoldChanges(dsd, fitExpToVar="Disease_status")
dxr1 = DEXSeq ...
written 12 days ago by
Lila M • 350
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... Hi guys I have a question for DEXseq results. After running it in R, I've just realized that some featuresIDs (e.g. E001) reported a p-value > 0.05. I'm wondering why DEXseq result consider this feature as differential y usage in therms of exons.
Is because of the log2fold? Is correct if I filte ...
written 12 days ago by
Lila M • 350
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... Ok, many thanks for this tip!!!
...
written 18 days ago by
Lila M • 350
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... But is less expressed in recurred? I understand that if I've included as treatment: control and recurred, and by default R will choose as reference level the factors based on alphabetical order, control should be my reference level and in that case, recurred is less expressed than control. Is this ...
written 18 days ago by
Lila M • 350
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... Thank you for the information, as is the first time that I have to deal with it, could you please help me to understand the results based on log2FoldChange?
ID log2FoldChange pvalue
ENSG00000132002.6 -1.3096108594 6.38592315283661E-15
ENSG00000188517.13 2.56893344 ...
written 18 days ago by
Lila M • 350
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... Hi guys, I have an issue... I'm doing some analysis using DESEq2. By default I know that when I create the object dds using
dds <- DESeqDataSetFromMatrix(countData = count.table,
colData = data.frame(treatment=treatment),
design = ~ treatment)
an as treatment (control vs recur ...
written 18 days ago by
Lila M • 350
• updated
18 days ago by
Devon Ryan ♦ 70k
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Comment:
C: DEXSeq transcripts per condition
... It is ok, if you want to select the transcripts affected by different condition, you can select the coordinates and the Gene ID from the result table and look them into a browser as ensemble, USCS or biomaRt (R), it will give you the transcript associated to these genes. Good Luck! ...
written 19 days ago by
Lila M • 350
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