User: Lila M

gravatar for Lila M
Lila M 350
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350
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Location:
UK
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2 days, 5 hours ago
Joined:
1 year, 11 months ago
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Posts by Lila M

<prev • 189 results • page 1 of 19 • next >
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Comment: C: what is the best way annotate the genes in a data frame?
... Thank you very much for this extensive explanation! ...
written 6 days ago by Lila M 350
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what is the best way annotate the genes in a data frame?
... 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 ...
R biomart annotation data frame written 9 days ago by Lila M 350 • updated 8 days ago by Kevin Blighe1.2k
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Comment: C: How to interpret DEXseq results in therms of significance
... 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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Comment: C: How to interpret DEXseq results in therms of significance
... 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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How to interpret DEXseq results in therms of significance
... 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 ...
dexseq exon rna-seq written 12 days ago by Lila M 350
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Comment: C: Differential expressed genes in DESeq
... Ok, many thanks for this tip!!! ...
written 18 days ago by Lila M 350
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Comment: C: Differential expressed genes in DESeq
... 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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Comment: C: Differential expressed genes in DESeq
... 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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Differential expressed genes in DESeq
... 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 ...
expression rna deseq rna-seq written 18 days ago by Lila M 350 • updated 18 days ago by Devon Ryan70k
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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

Latest awards to Lila M

Popular Question 6 weeks ago, created a question with more than 1,000 views. For how to compare 2 fasta sequences with perl
Popular Question 7 weeks ago, created a question with more than 1,000 views. For How to convert bedgraph to bigwig?
Scholar 4 months ago, created an answer that has been accepted. For A: How to plot a heat map for the top 30 differentially expressed genes.
Centurion 6 months ago, created 100 posts.
Supporter 6 months ago, voted at least 25 times.

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