User: Assa Yeroslaviz

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Assa Yeroslaviz1.3k
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Munich, Germany
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Posts by Assa Yeroslaviz

<prev • 261 results • page 1 of 27 • next >
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pheatmap - Error in do_one(nmeth) : NA/NaN/Inf in foreign function call (arg 1)
... I am trying to plot a heatmap using pheatmap().  I'm using the following script to set the parameters and plot the various clusters.  hmx.parameters <- list(counts_filtered_df, color = col.pal, cellwidth = 15, cellheight = 12, scale = "none", treeheight_row = 200, kmeans_k = ...
kmeans pheatmap written 3 days ago by Assa Yeroslaviz1.3k
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Comment: C: deseq2 correcting for batch effects
... my resultsNames() shows  > resultsNames(dds.date) [1] "Intercept" "date_d2_vs_d1" "condition_treatment_vs_control" I guess it takes the last position, which is  "condition_treatment_vs_control". So basically, what I analyse in the batch-controlled design ...
written 9 days ago by Assa Yeroslaviz1.3k • updated 9 days ago by Michael Love14k
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deseq2 correcting for batch effects
... I have a data set of six samples with 3x2 conditions.  > colData(dds) DataFrame with 8 rows and 3 columns sample.ID condition date <factor> <factor> <factor> S1 S1 control d1 S2 S2 treatment d1 S3 S3 control d1 S4 S ...
deseq2 removebatcheffect() batch effect design matrix written 9 days ago by Assa Yeroslaviz1.3k • updated 9 days ago by Michael Love14k
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Comment: C: read.maimages
... Hi Gordon, Thanks for the answer, but the question is over 5 years old. You have already answered this one then. May I ask why now? ...
written 10 days ago by Assa Yeroslaviz1.3k
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DESeq2 for ChIP on chip microarrays
... I would like to know if it is possible to use DESeq2 to analyze NimbleGene microarrays. I have a dataset of several conditions with enriched (IP) and control (Input) sample for several knock-outs. We would like to try and identify enriched probes (= this is what equals the gene name on the microarra ...
microarray limma deseq2 nimblegene ratio written 10 days ago by Assa Yeroslaviz1.3k • updated 10 days ago by Michael Love14k
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Comment: C: saving a plot as png and also showing inside Rstudio
... AFAIK you'll need to run the plotMDS command outside of the png() ... dev.off() structure again to make it visible in RStudio.  ...
written 10 days ago by Assa Yeroslaviz1.3k
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Comment: C: Error in tximport, unused argument (reader = read_tsv)
... did you try it without the parameter? ...
written 23 days ago by Assa Yeroslaviz1.3k
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Comment: C: RangedSummarizedExperiment in Deseq2 and DESeqDataSetFromMatrix
... is your count data stored in exp or ecp?   ...
written 23 days ago by Assa Yeroslaviz1.3k
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Answer: A: RangedSummarizedExperiment in Deseq2 and DESeqDataSetFromMatrix
... that is correct. try str(dds ) from the example and than also str(mydds) from your data and see if they have the same strucutre.   but to make your life easier Michael Love already created a package to import Kallisto data into DESeq2. take a look here ...
written 23 days ago by Assa Yeroslaviz1.3k
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Comment: C: converting a GRangesList object with different lengths into a data frame
... Thanks for  the suggestion of this function. It is worth knowing for later cases. I know about the problem of exon, luckily we are working on S. cerevisiae and have no introns problem, as we are interested in the complete transcript. But this function looks very interesting. ...
written 5 weeks ago by Assa Yeroslaviz1.3k

Latest awards to Assa Yeroslaviz

Appreciated 6 months ago, created a post with more than 5 votes. For A: Problem with biomart's listMarts function
Popular Question 6 months ago, created a question with more than 1,000 views. For extract intensity values from AffyBatch
Popular Question 8 months ago, created a question with more than 1,000 views. For DESeq2 produces adjusted p-values = 1
Popular Question 18 months ago, created a question with more than 1,000 views. For DESeq2 produces adjusted p-values = 1
Popular Question 18 months ago, created a question with more than 1,000 views. For could not find symbol "keepNA" in environment of the generic function
Good Answer 18 months ago, created an answer that was upvoted at least 5 times. For A: Problem with biomart's listMarts function
Appreciated 18 months ago, created a post with more than 5 votes. For A: Problem with biomart's listMarts function
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Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Problem with biomart's listMarts function
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Problem with biomart's listMarts function
Popular Question 2.0 years ago, created a question with more than 1,000 views. For could not find symbol "keepNA" in environment of the generic function
Scholar 2.3 years ago, created an answer that has been accepted. For A: could not find symbol "keepNA" in environment of the generic function
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