User: star

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star230
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Posts by star

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Kruskal Wallis test with the same p-value for all data?
... I have a table like below. I calculated the Kruskal Wallis test on it to find the difference between time points, but I observed the same p-value for all rows. I would like to know is it normal or there is something wrong? set: coordinate T1 T2 T3 1:12740 ...
R non-parametric statistic kruskal-wallis written 7 weeks ago by star230 • updated 7 weeks ago by i.sudbery7.3k
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Comment: C: Repeated Measure ANOVA, GLM,GEE, Linear mixed model, Generalized linear mixed mo
... Thank for the reply! Do you mean that I consider each time point as an independent sample and apply comparison? but does it work when I don't have any replicate? ...
written 8 weeks ago by star230
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Comment: C: Repeated Measure ANOVA, GLM,GEE, Linear mixed model, Generalized linear mixed mo
... Thank for the reply! Yes, it is normalized data (based on TPM) from different histone marks and from different time points. But here I only showed one histone mark. is there any way to do comparisons for each row over different time points? ...
written 8 weeks ago by star230
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Repeated Measure ANOVA, GLM,GEE, Linear mixed model, Generalized linear mixed model?
... I have a table like below (it is a small subset of my data. In this table, I measured one variable over 4 different time points (T1,..., T4), now I would like to check is there any significant difference between time points for each sample? Then based on that I will select those samples that have va ...
lme statistic glm anova written 8 weeks ago by star230 • updated 8 weeks ago by ATpoint32k
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How extract gene TPM from GTEx?
... I would like to know, is there any way to download Gene TPM data from GTEX from different part of the Brain? I have downloaded 'GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_tpm.gct.gz' an 'GTEx_Analysis_v8_Annotations_SampleAttributesDD.xlsx' files `https://www.gtexportal.org/home/datasets`, but ...
gtex gene_expression rna-seq written 9 weeks ago by star230 • updated 9 weeks ago by H.Hasani880
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Comment: C: Get GC content, Conservation score and repeat fraction from UCSC?
... @Many Thanks Luis. I have two more questions: - What is the difference between PhastCons100way and PhastConsElements100way? and which one should be used? - I could not find 'phastCons100way.valueAverage', there is only phastCons100way.value' that is for 100 specious when I check the output file, ...
written 11 weeks ago by star230
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Comment: C: Get GC content, Conservation score and repeat fraction from UCSC?
... @ Pierre. sorry I forgot to indicate that I would like to download (GC.conservation and ..) from UCSC. I edited the question. ...
written 11 weeks ago by star230
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Get GC content, Conservation score and repeat fraction from UCSC?
... I have a big genomic file including coordinate as below. Data: chr10 42383177 42384128 chr10 42384129 42385080 chr10 42385081 42386032 chr10 42386033 42386984 chr10 42386985 42387936 chr10 42387937 42388888 chr10 42388889 42389840 chr10 42389841 42390793 I would l ...
enrichment genomic integration ucsc written 11 weeks ago by star230 • updated 11 weeks ago by Luis Nassar360
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Comment: C: why the TPM value is not same?
... I want to divide RPK per-sample RPK based on the below explanation: 1) Divide the read counts by the length of each gene in kilobases. This gives you reads per kilobase (RPK). 2) Count up all the RPK values in a sample and divide this number by 1,000,000. This is your “per million” scaling factor. ...
written 3 months ago by star230
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Comment: C: why the TPM value is not same?
... Thanks for your reply! Yes, I have removed it and Edited the cod now. In my cod I just used transpose : `TPM <- t(t(RPK)*1e6 / colSums(RPK))` and it looks work. but I don`t know what exactly happens after two times transposing? ...
written 3 months ago by star230

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