User: deena

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deena10
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New User
Location:
Germany
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1 year, 2 months ago
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3 years, 9 months ago
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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 14 months ago by deena10
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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 14 months ago by deena10
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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 14 months ago by deena10 • updated 14 months ago by Michael Love20k
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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 15 months ago by deena10 • updated 15 months ago by Michael Love20k
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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 21 months ago by deena10
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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 21 months ago by deena10
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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 21 months ago by deena10
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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 21 months ago by deena10 • updated 21 months ago by Michael Love20k
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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 21 months ago by deena10
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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 21 months ago by deena10 • updated 21 months ago by Bernd Klaus520

Latest awards to deena

Great Question 21 months ago, created a question with more than 5,000 views. For logfoldStandard Error and wald-statistics in DESeq2 results
Popular Question 3.8 years ago, created a question with more than 1,000 views. For logfoldStandard Error and wald-statistics in DESeq2 results

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