User: mimA

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mimA20
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New User
Location:
European Union
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6 months, 3 weeks ago
Joined:
5 years, 5 months ago
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Posts by mimA

<prev • 14 results • page 1 of 2 • next >
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Comment: C: Calculating z-scores and p-values from ratios
... ok will do that, thank you! ...
written 7 months ago by mimA20
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Comment: C: Calculating z-scores and p-values from ratios
... I have mass spec data which represents proteins in quan values. These values are quite big (in thousands ex. 1000, 1300 2200 and so on). I have been told by our proteomics facility that no further normalisation is required for this data. However, since we wanted expression levels relative to our con ...
written 7 months ago by mimA20
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Comment: C: Calculating z-scores and p-values from ratios
... Thanks for your answer Petr. The only thing I'm concerned about is whether its acceptable to use ratios for example like I calculated by dividing with control and use those numbers directly to calculate p-values for example using something like limma?In this way the levels of proteins in each treatm ...
written 7 months ago by mimA20
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Comment: C: Calculating z-scores and p-values from ratios
... Thanks for your answer Petr. The only thing I'm concerned about is whether its acceptable to use ratios for example like I calculated by dividing with control and use those numbers directly to calculate p-values for example using something like limma?In this way the levels of proteins in each treatm ...
written 7 months ago by mimA20
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Comment: C: Calculating z-scores and p-values from ratios
... Thanks a lot for your reply Shunyip. But I'm just wondering z-score is calculated as (x-mean)/sd. Here x then becomes log2FC values so i end up with 2 z-scores for each protein again ...
written 7 months ago by mimA20
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Calculating z-scores and p-values from ratios
... Hello all, I have a question that I can't seem to figure out. I have protein data for 2 different treatments (3 samples each) and only 1 control sample. I want to run some statistics to find differences between the 2 treatment conditions but using the control because it is important for this experi ...
proteomics z-scores p-values statistics written 7 months ago by mimA20 • updated 7 months ago by Petr Ponomarenko2.4k
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Comment: C: Exon Array Analysis Tools
... Hi Nathan, Just wanted to ask does this do gene-level analysis on exon arrays? Thanks! ...
written 9 months ago by mimA20
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Comment: C: p-value and adjusted p-value exactly the same
... ok, will use Limma, thank you!! ...
written 9 months ago by mimA20
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Comment: C: p-value and adjusted p-value exactly the same
... Hi Devon, Thanks for your answer! You were right there was an error in my code somewhere. I fixed it so now the 2 values are not the same. About your comment on using Limma. I didn't exactly follow. You don't think using just a simple t-test and then adjusting for multiple comparisons is advisable? ...
written 9 months ago by mimA20
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p-value and adjusted p-value exactly the same
... Hi all, I'm analysing some microarray data and just calculated p-values using a t-test between 2 conditions (each with 3 replicates; total number of genes 14000). My p-values and adjusted p-values are coming out exactly the same. I've tried both FDR and bonferroni for correction using the p.adjust ...
R microarray written 9 months ago by mimA20 • updated 9 months ago by Dan Gaston6.8k

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