It is difficult to draw any conclusion without further experimentation. There may be many other factors that prevent the expression of the gene including factors like post-transcriptional regulators.

1. You can verify how many genes are there whose expression is not in accordance with the histone marks. If this for a small number of genes then you can investigate them separately. Use a statistical test to verify the significance of your correlation between histone mark and expression. If the discordance is widespread, then I would suggest you to repeat the RNAseq (easier and cheaper than repeating ChIP-seq). BTW, how were the read qualities? Depending on that you can decide which experiment needs repetition. Repetition will help you to know if the observation is indeed correct (a biological replicate).

2. If a few genes show discordance, then just do Real-Time PCR for these genes. RT-PCR is more sensitive and another technique of quantification is anyways good. Use a few concordant genes also, in the experiment.

It is difficult to draw any conclusion without further experimentation. There may be many other factors that prevent the expression of the gene including factors like post-transcriptional regulators. Some histone modifications like the ones you are mentioning are also a bit dicey and there can be bivalent modifications too. However, if there is a strong reason to speculate that these marks are associated with repression then you can try these:

1. You can verify how many genes are there whose expression is not in accordance with the histone marks. If this for a small number of genes then you can investigate them separately. Use a statistical test to verify the significance of your correlation between histone mark and expression. If the discordance is widespread, then I would suggest you to repeat the RNAseq (easier and cheaper than repeating ChIP-seq). BTW, how were the read qualities? Depending on that you can decide which experiment needs repetition. Repetition will help you to know if the observation is indeed correct (a biological replicate); possibly you may end also up concluding that these marks are actually dicey.

2. If a few genes show discordance, then just do Real-Time PCR for these genes. RT-PCR is more sensitive and another technique of quantification is anyways good. Use a few concordant genes also, in the experiment.

It is difficult to draw any conclusion without further experimentation. There may be many other factors that prevent the expression of the gene including factors like post-transcriptional regulators.

1. You can verify how many genes are there whose expression is not in accordance with the histone marks. If this for a small number of genes then you can investigate them separately. Use a statistical test to verify the significance of your correlation between histone mark and expression. If the discordance is widespread, then I would suggest you to repeat the RNAseq (easier and cheaper than repeating ChIP-seq). BTW, how were the read qualities? Depending on that you can decide which experiment needs repetition.

2. If a few genes show discordance, then just do Real-Time PCR for these genes. RT-PCR is more sensitive and another technique of quantification is anyways good. Use a few concordant genes also, in the experiment.

It is difficult to draw any conclusion without further experimentation. There may be many other factors that prevent the expression of the gene including factors like post-transcriptional regulators.

1. You can verify how many genes are there whose expression is not in accordance with the histone marks. If this for a small number of genes then you can investigate them separately. Use a statistical test to verify the significance of your correlation between histone mark and expression. If the discordance is widespread, then I would suggest you to repeat the RNAseq (easier and cheaper than repeating ChIP-seq). BTW, how were the read qualities? Depending on that you can decide which experiment needs repetition. Repetition will help you to know if the observation is indeed correct (a biological replicate).

2. If a few genes show discordance, then just do Real-Time PCR for these genes. RT-PCR is more sensitive and another technique of quantification is anyways good. Use a few concordant genes also, in the experiment.