User: Assa Yeroslaviz

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Assa Yeroslaviz1.3k
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Munich, Germany
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11 years, 10 months ago
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Posts by Assa Yeroslaviz

<prev • 265 results • page 1 of 27 • next >
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Comment: C: complex design for chip-seq analysis
... Thanks for the answer and the reference. But I am not sure, what you mean by that. How can I ignore the Input file, after running a peak caller. I did use MACS2 to call for peaks. But how do I get the counts per Gene/Transcript/TSS after running a peak caller? I know I can get the counts from a ba ...
written 7 weeks ago by Assa Yeroslaviz1.3k
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Comment: C: complex design for chip-seq analysis
... Thanks Aaron for the really elaborate answer. So if I understand it correctly, it is ok to use edgeR (and for that case also DESeq) with ChIP-Seq data? I thought it was meant only for RNA-Seq, as the reads are Poisson distributed and not negative binomial. Am I wrong with this assumption? Another d ...
written 7 weeks ago by Assa Yeroslaviz1.3k
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resize functions causes an error - "could not find function "unsafe.update"
... When running the resize function, I keep getting the following error message: > tAE <- IRanges::resize(tA, 200, fix = "center") Error in unsafe.update(object, ...) : could not find function "unsafe.update"   I have read that this might happens when you have older packages conflicted wi ...
iranges genomicranges resize written 7 weeks ago by Assa Yeroslaviz1.3k
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complex design for chip-seq analysis
... I have a chip-seq data set with three conditions (wt , KO1, KO2) and three time points (0h, 2h, 4h). For each condition and TP I have duplicated samples for IP and Input samples, which looks like that: condition TP Replicate IP Input wt 0h 1 IP Input ...
chipseq limma multiple factor design design matrix csaw written 7 weeks ago by Assa Yeroslaviz1.3k • updated 7 weeks ago by Aaron Lun17k
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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 8 weeks 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 weeks ago by Assa Yeroslaviz1.3k • updated 9 weeks ago by Michael Love15k
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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 weeks ago by Assa Yeroslaviz1.3k • updated 9 weeks ago by Michael Love15k
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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 9 weeks 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 9 weeks ago by Assa Yeroslaviz1.3k • updated 9 weeks ago by Michael Love15k
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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 9 weeks ago by Assa Yeroslaviz1.3k

Latest awards to Assa Yeroslaviz

Appreciated 8 months ago, created a post with more than 5 votes. For A: Problem with biomart's listMarts function
Popular Question 8 months ago, created a question with more than 1,000 views. For extract intensity values from AffyBatch
Popular Question 10 months ago, created a question with more than 1,000 views. For DESeq2 produces adjusted p-values = 1
Popular Question 20 months ago, created a question with more than 1,000 views. For DESeq2 produces adjusted p-values = 1
Popular Question 20 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 20 months ago, created an answer that was upvoted at least 5 times. For A: Problem with biomart's listMarts function
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Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Problem with biomart's listMarts function
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Problem with biomart's listMarts function
Popular Question 2.2 years ago, created a question with more than 1,000 views. For could not find symbol "keepNA" in environment of the generic function
Scholar 2.4 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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