User: deena

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deena0
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Posts by deena

<prev • 13 results • page 1 of 2 • next >
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Comment: C: Obtaining transcript names in RSEM
... Hi I tried importing the RSEM.isoform.results files into R like described in vignette. My RSEM.isoform.result file has columns transcript_id gene_id effective_length expected_count TPM FPKM IsoPct. So when tried to import it got the following code list.files("~/Trinity_kallisto_RSEM/RSEM/","*.iso ...
written 8 weeks ago by deena0
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Comment: C: Obtaining transcript names in RSEM
... Hi Michael, Thank you very much for your reply. I am working on a non-model organism for which has denovo assembled transcriptome. I use Trinity suite to align and estimate the count data. Trinity suite can estimate counts using RSEM or kallisto depending upon the user's choice. In case of kallisto ...
written 8 weeks ago by deena0
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Obtaining transcript names in RSEM
... Hi, I have performed the abundance estimation using RSEM which outputted the genes.results and isoforms.results. I would like to import the isoforms results into DESeq2 pipeline. I followed the tximport pipleine for RSEM like following but when I checked the rownames, it gave me gene names instead ...
tximport rsem written 8 weeks ago by deena0 • updated 8 weeks ago by Michael Love15k
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Importing kallisto's abundance files into DESeq2 pipeline
... Hi, I am glad that tximport is introduced with option to import counts from kallisto, RSEM etc. I have 6 RNA-seq samples. I have quantified every sample using kallisto. For every sample, abundance.tsv file and abundance.h5 files were generated. Now in order to make use of kallisto abundance_estimat ...
deseq2 kallisto written 9 weeks ago by deena0 • updated 9 weeks ago by Michael Love15k
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Comment: C: Inspection and Correction of p-values in DESeq2 pipeline by Bernd
... HI Bernd, I tried to find batch effect on samples but it didnt seems to be like presence of batch effect. The historgrams of specific comparisons of a particular time point follows hill-shaped structure even after the fdr tool correction. The z-score computed for that specific results are z-Score(s ...
written 8 months ago by deena0
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Comment: C: Loading samples into DESeq2
... Thanks a lot Michael. The strange thing which I found this huge data is that many replicates particular samples in particular time point gets clustered with other samples of different time point. I havent observed such kind of clustering and I am wondering how to handle such replicate that dosent cl ...
written 8 months ago by deena0
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Comment: C: Loading samples into DESeq2
... Thank you Michael. You understood correctly my experimental design.  So far I have made a data frame called conditions in R like following Conditions Treated1_T2_1 Treated1_T2 Treated1_T2_2 Treated1_T2 Treated1_ ...
written 8 months ago by deena0
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Loading samples into DESeq2
... Hi all, I have a RNA seq data performed at different time points. So for every time I have 4 samples(Control, Knock-down_1, Knock-down_2, Knock-down_3). So all together there are 36 samples from all 3 time points. Now I want to compare every Knock-down sample within a particular time point to its ...
deseq2 written 8 months ago by deena0 • updated 8 months ago by Michael Love15k
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Comment: C: Inspection and Correction of p-values in DESeq2 pipeline by Bernd
... HI Michael, Like you said I have attached the the histogram of pvalues and the R code data = read.delim("raw_counts.txt", row.names=1) rnaseqMatrix = as.matrix(round(data)) conditions = data.frame(conditions=factor(c(rep("Control", 3), rep("gene_x_kd", 3), rep("gene_y_kd", 3), rep("genexy_kd", 3)) ...
written 8 months ago by deena0
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Inspection and Correction of p-values in DESeq2 pipeline by Bernd
... Hi Michael, I following a tutorial from Huber(http://www-huber.embl.de/users/klaus/Teaching/DESeq2Predoc2014.html) for detecting Diff.expressed genes using DESeq2. In the section, 10.2 Inspection and correction of p–values  it suggest that if the distribution of raw pvalues follows either hill-shap ...
deseq2 fdr fdrtool written 8 months ago by deena0 • updated 8 months ago by Bernd Klaus470

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Popular Question 2.7 years ago, created a question with more than 1,000 views. For logfoldStandard Error and wald-statistics in DESeq2 results

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